CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

Home

Methods

Datasets

Rankings

RNA 2D Atlas

Help

FAQ

Contact us

RSS feeds

Twitter

All short RNAs from the RNAstrand dataset

	All RNAs from RNAstrand dataset were used to benchmark RNA secondary structure prediction methods. Input for comparative methods consisted of a sequence collection / an alignment containing the query sequence and all sequences from a given seed alignment for an Rfam family identified for the query.
Updated: Oct. 3, 2012
Base pair definition: extended
Type of RNA structures: all (including pseudoknotted)
RNA sequence length range: 20, 200
Number of RNA sequences: 882
Robustness test: no

In the summary below ranks have been assigned only to methods, for which at least 40% of comparisons with other methods is valid (i.e. at least 40% (in case of this ranking: 21) of the comparisons were based on at least 10 predictions for common targets).

The ratio 40% / 60% was chosen in order not to bias methods for which not enough predictions have been collected.

Summary of pairwise comparisons

54 methods predicting RNA secondary structure were compared with each other (thus each method has 53 comparisons with other methods (sum of values from columns "Wins", "Losses", "=" and "?" in each row)).

Legend:

=	draw - it is assigned when both methods have generated >= 10 predictions for common targets if:
	1) the accuracies of their results are statistically not distinguishable (P-value greater than 0.001),
	or
	2) the numbers of base pairs classified to categories True Positivies (TP), True Negatives (TN), False Positivies (FP, including 3 subcategories) and False Negatives (FN) for both methods are the same.
?	two methods cannot be compared ("no winner") - not enough predictions for a given pair of methods (minimum is 10)
N/A	a method for which more than 32 (60%) of comparisons with other methods is invalid (see column "?").

Rank	Method Name	Trained	Wins	Losses	=	?	Predictions attempted	Predictions generated
1	ContextFold	yes	53	0	0	0	882	882
2	TurboFold(20)	no	51	1	0	1	320	320
3	CentroidAlifold(seed)	yes	49	3	1	0	501	216
4	CentroidHomfold‑LAST	yes	49	4	0	0	882	882
4	PETfold_pre2.0(seed)	no	49	4	0	0	501	498
6	TurboFold(seed)	no	48	3	2	0	501	33
7	MXScarna(seed)	no	47	6	0	0	501	233
8	CentroidAlifold(20)	yes	45	7	0	1	320	320
9	MXScarna(20)	no	43	9	0	1	320	320
9	PETfold_pre2.0(20)	no	43	9	0	1	320	320
11	PPfold(20)	yes	41	11	0	1	320	314
12	RSpredict(20)	no	39	12	1	1	320	320
12	RNAalifold(20)	no	39	12	1	1	320	320
14	IPknot	yes	39	14	0	0	882	882
15	Multilign(20)	no	37	15	0	1	320	311
16	CentroidFold	yes	35	17	1	0	882	882
17	Contrafold	yes	34	18	1	0	882	882
18	Murlet(20)	yes	33	19	0	1	320	319
18	RNASampler(20)	no	33	19	0	1	320	315
20	CMfinder(seed)	yes	32	17	4	0	501	78
21	MaxExpect	yes	32	20	1	0	882	882
22	CMfinder(20)	yes	31	19	2	1	320	316
23	CRWrnafold	yes	31	21	1	0	882	881
24	ProbKnot	yes	29	21	3	0	882	882
25	Mastr(20)	yes	27	21	4	1	320	320
26	Fold	no	27	24	2	0	882	882
27	UNAFold	no	26	26	1	0	882	882
28	PknotsRG	no	26	27	0	0	882	882
29	Sfold	no	24	29	0	0	882	882
30	RNAalifold(seed)	no	23	30	0	0	501	205
31	RNAsubopt	no	21	31	1	0	882	882
32	HotKnots	no	20	31	2	0	882	875
33	RNAfold	no	19	33	1	0	882	882
34	RNAshapes	no	18	32	3	0	882	882
34	RNASampler(seed)	no	18	32	3	0	501	86
36	Afold	no	18	33	2	0	882	530
37	Pknots	no	17	33	3	0	882	697
38	McQFold	yes	16	36	1	0	882	882
39	Carnac(20)	no	15	37	0	1	320	320
40	RNASLOpt	no	15	38	0	0	882	882
41	Cylofold	no	14	39	0	0	882	796
42	Multilign(seed)	no	13	23	3	14	501	13
43	RNAwolf	yes	9	43	1	0	882	882
44	PPfold(seed)	yes	8	42	2	1	501	40
45	Murlet(seed)	yes	8	40	5	0	501	91
46	Alterna	no	7	44	2	0	882	693
47	Carnac(seed)	no	7	45	1	0	501	123
48	Vsfold4	no	6	47	0	0	882	882
49	RSpredict(seed)	no	5	45	3	0	501	216
50	Vsfold5	no	5	48	0	0	882	882
51	RDfolder	no	4	47	2	0	882	693
52	MCFold	yes	3	47	3	0	882	761
53	NanoFolder	yes	2	49	0	2	882	117
54	Mastr(seed)	yes	1	51	1	0	501	234

Detailed results of pairwise comparisons between methods

Legend:

+	method on the left scored higher in this pairwise comparison
-	method on the left scored lower in this pairwise comparison
=	draw - it is assigned when both methods have generated >= 10 predictions for common targets if:
	1) the accuracies of their results are statistically not distinguishable (P-value greater than 0.001),
	or
	2) the numbers of base pairs classified to categories True Positivies (TP), True Negatives (TN), False Positivies (FP, including 3 subcategories) and False Negatives (FN) for both methods are the same.
?	two methods cannot be compared ("no winner") - not enough predictions for a given pair of methods (minimum is 10)

P-values were obtained using Wilcoxon signed-rank test taking 2 sets of 40 MCC values obtained for 40 random subsets of 90% of the dataset for each pair of methods. If the P-value is lower than 0.001 and there are at least 10 sequences on which benchmark was performed, the difference between the performance of two methods is assumed to be statistically sound.


ContextFold		+ ContextFold vs TurboFold(20) Matthews Correlation Coefficient ContextFold: 0.923 TurboFold(20): 0.889 Sensitivity ContextFold: 0.898 TurboFold(20): 0.861 Positive Predictive Value ContextFold: 0.949 TurboFold(20): 0.919 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs CentroidAlifold(seed) Matthews Correlation Coefficient ContextFold: 0.839 CentroidAlifold(seed): 0.790 Sensitivity ContextFold: 0.812 CentroidAlifold(seed): 0.699 Positive Predictive Value ContextFold: 0.868 CentroidAlifold(seed): 0.896 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs CentroidHomfold‑LAST Matthews Correlation Coefficient ContextFold: 0.779 CentroidHomfold‑LAST: 0.736 Sensitivity ContextFold: 0.741 CentroidHomfold‑LAST: 0.665 Positive Predictive Value ContextFold: 0.823 CentroidHomfold‑LAST: 0.818 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs PETfold_pre2.0(seed) Matthews Correlation Coefficient ContextFold: 0.893 PETfold_pre2.0(seed): 0.879 Sensitivity ContextFold: 0.864 PETfold_pre2.0(seed): 0.825 Positive Predictive Value ContextFold: 0.925 PETfold_pre2.0(seed): 0.938 Number of pairs reference - predicted secondary structure: 498 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs TurboFold(seed) Matthews Correlation Coefficient ContextFold: 0.822 TurboFold(seed): 0.798 Sensitivity ContextFold: 0.791 TurboFold(seed): 0.766 Positive Predictive Value ContextFold: 0.856 TurboFold(seed): 0.835 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs MXScarna(seed) Matthews Correlation Coefficient ContextFold: 0.843 MXScarna(seed): 0.750 Sensitivity ContextFold: 0.816 MXScarna(seed): 0.712 Positive Predictive Value ContextFold: 0.873 MXScarna(seed): 0.793 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs CentroidAlifold(20) Matthews Correlation Coefficient ContextFold: 0.923 CentroidAlifold(20): 0.849 Sensitivity ContextFold: 0.898 CentroidAlifold(20): 0.754 Positive Predictive Value ContextFold: 0.949 CentroidAlifold(20): 0.957 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs PETfold_pre2.0(20) Matthews Correlation Coefficient ContextFold: 0.923 PETfold_pre2.0(20): 0.847 Sensitivity ContextFold: 0.898 PETfold_pre2.0(20): 0.737 Positive Predictive Value ContextFold: 0.949 PETfold_pre2.0(20): 0.975 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs MXScarna(20) Matthews Correlation Coefficient ContextFold: 0.923 MXScarna(20): 0.838 Sensitivity ContextFold: 0.898 MXScarna(20): 0.791 Positive Predictive Value ContextFold: 0.949 MXScarna(20): 0.891 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs PPfold(20) Matthews Correlation Coefficient ContextFold: 0.923 PPfold(20): 0.839 Sensitivity ContextFold: 0.898 PPfold(20): 0.721 Positive Predictive Value ContextFold: 0.951 PPfold(20): 0.977 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNAalifold(20) Matthews Correlation Coefficient ContextFold: 0.923 RNAalifold(20): 0.816 Sensitivity ContextFold: 0.898 RNAalifold(20): 0.690 Positive Predictive Value ContextFold: 0.949 RNAalifold(20): 0.966 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RSpredict(20) Matthews Correlation Coefficient ContextFold: 0.923 RSpredict(20): 0.789 Sensitivity ContextFold: 0.898 RSpredict(20): 0.693 Positive Predictive Value ContextFold: 0.949 RSpredict(20): 0.901 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs IPknot Matthews Correlation Coefficient ContextFold: 0.779 IPknot: 0.694 Sensitivity ContextFold: 0.741 IPknot: 0.661 Positive Predictive Value ContextFold: 0.823 IPknot: 0.733 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Multilign(20) Matthews Correlation Coefficient ContextFold: 0.921 Multilign(20): 0.784 Sensitivity ContextFold: 0.896 Multilign(20): 0.697 Positive Predictive Value ContextFold: 0.948 Multilign(20): 0.885 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs CentroidFold Matthews Correlation Coefficient ContextFold: 0.779 CentroidFold: 0.645 Sensitivity ContextFold: 0.741 CentroidFold: 0.612 Positive Predictive Value ContextFold: 0.823 CentroidFold: 0.684 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Contrafold Matthews Correlation Coefficient ContextFold: 0.779 Contrafold: 0.643 Sensitivity ContextFold: 0.741 Contrafold: 0.634 Positive Predictive Value ContextFold: 0.823 Contrafold: 0.657 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNASampler(20) Matthews Correlation Coefficient ContextFold: 0.924 RNASampler(20): 0.770 Sensitivity ContextFold: 0.898 RNASampler(20): 0.622 Positive Predictive Value ContextFold: 0.951 RNASampler(20): 0.957 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Murlet(20) Matthews Correlation Coefficient ContextFold: 0.923 Murlet(20): 0.750 Sensitivity ContextFold: 0.898 Murlet(20): 0.619 Positive Predictive Value ContextFold: 0.950 Murlet(20): 0.913 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs CMfinder(seed) Matthews Correlation Coefficient ContextFold: 0.690 CMfinder(seed): 0.571 Sensitivity ContextFold: 0.632 CMfinder(seed): 0.439 Positive Predictive Value ContextFold: 0.758 CMfinder(seed): 0.747 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs MaxExpect Matthews Correlation Coefficient ContextFold: 0.779 MaxExpect: 0.633 Sensitivity ContextFold: 0.741 MaxExpect: 0.617 Positive Predictive Value ContextFold: 0.823 MaxExpect: 0.654 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs CMfinder(20) Matthews Correlation Coefficient ContextFold: 0.922 CMfinder(20): 0.735 Sensitivity ContextFold: 0.898 CMfinder(20): 0.603 Positive Predictive Value ContextFold: 0.949 CMfinder(20): 0.899 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs CRWrnafold Matthews Correlation Coefficient ContextFold: 0.779 CRWrnafold: 0.630 Sensitivity ContextFold: 0.741 CRWrnafold: 0.618 Positive Predictive Value ContextFold: 0.823 CRWrnafold: 0.648 Number of pairs reference - predicted secondary structure: 881 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs ProbKnot Matthews Correlation Coefficient ContextFold: 0.779 ProbKnot: 0.630 Sensitivity ContextFold: 0.741 ProbKnot: 0.622 Positive Predictive Value ContextFold: 0.823 ProbKnot: 0.644 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Mastr(20) Matthews Correlation Coefficient ContextFold: 0.923 Mastr(20): 0.708 Sensitivity ContextFold: 0.898 Mastr(20): 0.635 Positive Predictive Value ContextFold: 0.949 Mastr(20): 0.793 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Fold Matthews Correlation Coefficient ContextFold: 0.779 Fold: 0.628 Sensitivity ContextFold: 0.741 Fold: 0.620 Positive Predictive Value ContextFold: 0.823 Fold: 0.641 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs UNAFold Matthews Correlation Coefficient ContextFold: 0.779 UNAFold: 0.620 Sensitivity ContextFold: 0.741 UNAFold: 0.605 Positive Predictive Value ContextFold: 0.823 UNAFold: 0.639 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs PknotsRG Matthews Correlation Coefficient ContextFold: 0.779 PknotsRG: 0.617 Sensitivity ContextFold: 0.741 PknotsRG: 0.610 Positive Predictive Value ContextFold: 0.823 PknotsRG: 0.630 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Sfold Matthews Correlation Coefficient ContextFold: 0.779 Sfold: 0.618 Sensitivity ContextFold: 0.741 Sfold: 0.581 Positive Predictive Value ContextFold: 0.823 Sfold: 0.663 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNAalifold(seed) Matthews Correlation Coefficient ContextFold: 0.836 RNAalifold(seed): 0.610 Sensitivity ContextFold: 0.809 RNAalifold(seed): 0.404 Positive Predictive Value ContextFold: 0.866 RNAalifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNAsubopt Matthews Correlation Coefficient ContextFold: 0.779 RNAsubopt: 0.615 Sensitivity ContextFold: 0.741 RNAsubopt: 0.609 Positive Predictive Value ContextFold: 0.823 RNAsubopt: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs HotKnots Matthews Correlation Coefficient ContextFold: 0.779 HotKnots: 0.613 Sensitivity ContextFold: 0.740 HotKnots: 0.607 Positive Predictive Value ContextFold: 0.822 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 875 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNAfold Matthews Correlation Coefficient ContextFold: 0.779 RNAfold: 0.612 Sensitivity ContextFold: 0.741 RNAfold: 0.604 Positive Predictive Value ContextFold: 0.823 RNAfold: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNAshapes Matthews Correlation Coefficient ContextFold: 0.779 RNAshapes: 0.612 Sensitivity ContextFold: 0.741 RNAshapes: 0.602 Positive Predictive Value ContextFold: 0.823 RNAshapes: 0.628 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNASampler(seed) Matthews Correlation Coefficient ContextFold: 0.692 RNASampler(seed): 0.557 Sensitivity ContextFold: 0.637 RNASampler(seed): 0.389 Positive Predictive Value ContextFold: 0.755 RNASampler(seed): 0.802 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Afold Matthews Correlation Coefficient ContextFold: 0.718 Afold: 0.558 Sensitivity ContextFold: 0.673 Afold: 0.541 Positive Predictive Value ContextFold: 0.770 Afold: 0.582 Number of pairs reference - predicted secondary structure: 530 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Pknots Matthews Correlation Coefficient ContextFold: 0.763 Pknots: 0.606 Sensitivity ContextFold: 0.721 Pknots: 0.595 Positive Predictive Value ContextFold: 0.811 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs McQFold Matthews Correlation Coefficient ContextFold: 0.779 McQFold: 0.583 Sensitivity ContextFold: 0.741 McQFold: 0.557 Positive Predictive Value ContextFold: 0.823 McQFold: 0.616 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Carnac(20) Matthews Correlation Coefficient ContextFold: 0.923 Carnac(20): 0.675 Sensitivity ContextFold: 0.898 Carnac(20): 0.500 Positive Predictive Value ContextFold: 0.949 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RNASLOpt Matthews Correlation Coefficient ContextFold: 0.779 RNASLOpt: 0.562 Sensitivity ContextFold: 0.741 RNASLOpt: 0.521 Positive Predictive Value ContextFold: 0.823 RNASLOpt: 0.613 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Cylofold Matthews Correlation Coefficient ContextFold: 0.804 Cylofold: 0.577 Sensitivity ContextFold: 0.764 Cylofold: 0.554 Positive Predictive Value ContextFold: 0.849 Cylofold: 0.608 Number of pairs reference - predicted secondary structure: 796 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Multilign(seed) Matthews Correlation Coefficient ContextFold: 0.568 Multilign(seed): 0.485 Sensitivity ContextFold: 0.512 Multilign(seed): 0.386 Positive Predictive Value ContextFold: 0.640 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.93248927742e-08	+ ContextFold vs RNAwolf Matthews Correlation Coefficient ContextFold: 0.779 RNAwolf: 0.518 Sensitivity ContextFold: 0.741 RNAwolf: 0.523 Positive Predictive Value ContextFold: 0.823 RNAwolf: 0.520 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs PPfold(seed) Matthews Correlation Coefficient ContextFold: 0.868 PPfold(seed): 0.380 Sensitivity ContextFold: 0.845 PPfold(seed): 0.170 Positive Predictive Value ContextFold: 0.894 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Murlet(seed) Matthews Correlation Coefficient ContextFold: 0.718 Murlet(seed): 0.468 Sensitivity ContextFold: 0.666 Murlet(seed): 0.266 Positive Predictive Value ContextFold: 0.777 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Alterna Matthews Correlation Coefficient ContextFold: 0.765 Alterna: 0.552 Sensitivity ContextFold: 0.723 Alterna: 0.547 Positive Predictive Value ContextFold: 0.814 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Carnac(seed) Matthews Correlation Coefficient ContextFold: 0.787 Carnac(seed): 0.415 Sensitivity ContextFold: 0.744 Carnac(seed): 0.196 Positive Predictive Value ContextFold: 0.835 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Vsfold4 Matthews Correlation Coefficient ContextFold: 0.779 Vsfold4: 0.487 Sensitivity ContextFold: 0.741 Vsfold4: 0.447 Positive Predictive Value ContextFold: 0.823 Vsfold4: 0.537 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RSpredict(seed) Matthews Correlation Coefficient ContextFold: 0.839 RSpredict(seed): 0.373 Sensitivity ContextFold: 0.812 RSpredict(seed): 0.251 Positive Predictive Value ContextFold: 0.868 RSpredict(seed): 0.562 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Vsfold5 Matthews Correlation Coefficient ContextFold: 0.779 Vsfold5: 0.477 Sensitivity ContextFold: 0.741 Vsfold5: 0.450 Positive Predictive Value ContextFold: 0.823 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs RDfolder Matthews Correlation Coefficient ContextFold: 0.765 RDfolder: 0.520 Sensitivity ContextFold: 0.723 RDfolder: 0.464 Positive Predictive Value ContextFold: 0.814 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs MCFold Matthews Correlation Coefficient ContextFold: 0.771 MCFold: 0.473 Sensitivity ContextFold: 0.731 MCFold: 0.524 Positive Predictive Value ContextFold: 0.817 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs NanoFolder Matthews Correlation Coefficient ContextFold: 0.839 NanoFolder: 0.335 Sensitivity ContextFold: 0.799 NanoFolder: 0.384 Positive Predictive Value ContextFold: 0.882 NanoFolder: 0.301 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ContextFold vs Mastr(seed) Matthews Correlation Coefficient ContextFold: 0.844 Mastr(seed): 0.263 Sensitivity ContextFold: 0.817 Mastr(seed): 0.089 Positive Predictive Value ContextFold: 0.874 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08
TurboFold(20)	320 ContextFold vs TurboFold(20) Matthews Correlation Coefficient ContextFold: 0.923 TurboFold(20): 0.889 Sensitivity ContextFold: 0.898 TurboFold(20): 0.861 Positive Predictive Value ContextFold: 0.949 TurboFold(20): 0.919 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ TurboFold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient TurboFold(20): 0.830 CentroidAlifold(seed): 0.815 Sensitivity TurboFold(20): 0.812 CentroidAlifold(seed): 0.743 Positive Predictive Value TurboFold(20): 0.850 CentroidAlifold(seed): 0.897 Number of pairs reference - predicted secondary structure: 141 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient TurboFold(20): 0.889 CentroidHomfold‑LAST: 0.858 Sensitivity TurboFold(20): 0.861 CentroidHomfold‑LAST: 0.821 Positive Predictive Value TurboFold(20): 0.919 CentroidHomfold‑LAST: 0.900 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient TurboFold(20): 0.890 PETfold_pre2.0(seed): 0.885 Sensitivity TurboFold(20): 0.862 PETfold_pre2.0(seed): 0.832 Positive Predictive Value TurboFold(20): 0.920 PETfold_pre2.0(seed): 0.944 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 7.5939721025e-08	+ TurboFold(20) vs TurboFold(seed) Matthews Correlation Coefficient TurboFold(20): 0.885 TurboFold(seed): 0.880 Sensitivity TurboFold(20): 0.880 TurboFold(seed): 0.875 Positive Predictive Value TurboFold(20): 0.891 TurboFold(seed): 0.886 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.70887622364e-08	+ TurboFold(20) vs MXScarna(seed) Matthews Correlation Coefficient TurboFold(20): 0.839 MXScarna(seed): 0.792 Sensitivity TurboFold(20): 0.818 MXScarna(seed): 0.756 Positive Predictive Value TurboFold(20): 0.862 MXScarna(seed): 0.832 Number of pairs reference - predicted secondary structure: 153 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs CentroidAlifold(20) Matthews Correlation Coefficient TurboFold(20): 0.889 CentroidAlifold(20): 0.849 Sensitivity TurboFold(20): 0.861 CentroidAlifold(20): 0.754 Positive Predictive Value TurboFold(20): 0.919 CentroidAlifold(20): 0.957 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs PETfold_pre2.0(20) Matthews Correlation Coefficient TurboFold(20): 0.889 PETfold_pre2.0(20): 0.847 Sensitivity TurboFold(20): 0.861 PETfold_pre2.0(20): 0.737 Positive Predictive Value TurboFold(20): 0.919 PETfold_pre2.0(20): 0.975 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(20): 0.889 MXScarna(20): 0.838 Sensitivity TurboFold(20): 0.861 MXScarna(20): 0.791 Positive Predictive Value TurboFold(20): 0.919 MXScarna(20): 0.891 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs PPfold(20) Matthews Correlation Coefficient TurboFold(20): 0.890 PPfold(20): 0.839 Sensitivity TurboFold(20): 0.862 PPfold(20): 0.721 Positive Predictive Value TurboFold(20): 0.921 PPfold(20): 0.977 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RNAalifold(20) Matthews Correlation Coefficient TurboFold(20): 0.889 RNAalifold(20): 0.816 Sensitivity TurboFold(20): 0.861 RNAalifold(20): 0.690 Positive Predictive Value TurboFold(20): 0.919 RNAalifold(20): 0.966 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(20): 0.889 RSpredict(20): 0.789 Sensitivity TurboFold(20): 0.861 RSpredict(20): 0.693 Positive Predictive Value TurboFold(20): 0.919 RSpredict(20): 0.901 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs IPknot Matthews Correlation Coefficient TurboFold(20): 0.889 IPknot: 0.783 Sensitivity TurboFold(20): 0.861 IPknot: 0.761 Positive Predictive Value TurboFold(20): 0.919 IPknot: 0.807 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Multilign(20) Matthews Correlation Coefficient TurboFold(20): 0.889 Multilign(20): 0.784 Sensitivity TurboFold(20): 0.860 Multilign(20): 0.697 Positive Predictive Value TurboFold(20): 0.920 Multilign(20): 0.885 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs CentroidFold Matthews Correlation Coefficient TurboFold(20): 0.889 CentroidFold: 0.735 Sensitivity TurboFold(20): 0.861 CentroidFold: 0.710 Positive Predictive Value TurboFold(20): 0.919 CentroidFold: 0.764 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Contrafold Matthews Correlation Coefficient TurboFold(20): 0.889 Contrafold: 0.733 Sensitivity TurboFold(20): 0.861 Contrafold: 0.729 Positive Predictive Value TurboFold(20): 0.919 Contrafold: 0.740 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RNASampler(20) Matthews Correlation Coefficient TurboFold(20): 0.891 RNASampler(20): 0.770 Sensitivity TurboFold(20): 0.863 RNASampler(20): 0.622 Positive Predictive Value TurboFold(20): 0.921 RNASampler(20): 0.957 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Murlet(20) Matthews Correlation Coefficient TurboFold(20): 0.890 Murlet(20): 0.750 Sensitivity TurboFold(20): 0.862 Murlet(20): 0.619 Positive Predictive Value TurboFold(20): 0.920 Murlet(20): 0.913 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs CMfinder(seed) Matthews Correlation Coefficient TurboFold(20): 0.744 CMfinder(seed): 0.736 Sensitivity TurboFold(20): 0.678 CMfinder(seed): 0.607 Positive Predictive Value TurboFold(20): 0.821 CMfinder(seed): 0.898 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 2.89205881697e-05	+ TurboFold(20) vs MaxExpect Matthews Correlation Coefficient TurboFold(20): 0.889 MaxExpect: 0.711 Sensitivity TurboFold(20): 0.861 MaxExpect: 0.701 Positive Predictive Value TurboFold(20): 0.919 MaxExpect: 0.725 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs CMfinder(20) Matthews Correlation Coefficient TurboFold(20): 0.890 CMfinder(20): 0.735 Sensitivity TurboFold(20): 0.862 CMfinder(20): 0.603 Positive Predictive Value TurboFold(20): 0.920 CMfinder(20): 0.899 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs CRWrnafold Matthews Correlation Coefficient TurboFold(20): 0.889 CRWrnafold: 0.783 Sensitivity TurboFold(20): 0.861 CRWrnafold: 0.771 Positive Predictive Value TurboFold(20): 0.919 CRWrnafold: 0.798 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs ProbKnot Matthews Correlation Coefficient TurboFold(20): 0.889 ProbKnot: 0.707 Sensitivity TurboFold(20): 0.861 ProbKnot: 0.702 Positive Predictive Value TurboFold(20): 0.919 ProbKnot: 0.716 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Mastr(20) Matthews Correlation Coefficient TurboFold(20): 0.889 Mastr(20): 0.708 Sensitivity TurboFold(20): 0.861 Mastr(20): 0.635 Positive Predictive Value TurboFold(20): 0.919 Mastr(20): 0.793 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Fold Matthews Correlation Coefficient TurboFold(20): 0.889 Fold: 0.712 Sensitivity TurboFold(20): 0.861 Fold: 0.710 Positive Predictive Value TurboFold(20): 0.919 Fold: 0.717 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs UNAFold Matthews Correlation Coefficient TurboFold(20): 0.889 UNAFold: 0.708 Sensitivity TurboFold(20): 0.861 UNAFold: 0.696 Positive Predictive Value TurboFold(20): 0.919 UNAFold: 0.723 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs PknotsRG Matthews Correlation Coefficient TurboFold(20): 0.889 PknotsRG: 0.691 Sensitivity TurboFold(20): 0.861 PknotsRG: 0.687 Positive Predictive Value TurboFold(20): 0.919 PknotsRG: 0.699 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Sfold Matthews Correlation Coefficient TurboFold(20): 0.889 Sfold: 0.698 Sensitivity TurboFold(20): 0.861 Sfold: 0.662 Positive Predictive Value TurboFold(20): 0.919 Sfold: 0.740 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RNAalifold(seed) Matthews Correlation Coefficient TurboFold(20): 0.829 RNAalifold(seed): 0.604 Sensitivity TurboFold(20): 0.810 RNAalifold(seed): 0.383 Positive Predictive Value TurboFold(20): 0.850 RNAalifold(seed): 0.956 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RNAsubopt Matthews Correlation Coefficient TurboFold(20): 0.889 RNAsubopt: 0.694 Sensitivity TurboFold(20): 0.861 RNAsubopt: 0.693 Positive Predictive Value TurboFold(20): 0.919 RNAsubopt: 0.700 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs HotKnots Matthews Correlation Coefficient TurboFold(20): 0.889 HotKnots: 0.698 Sensitivity TurboFold(20): 0.861 HotKnots: 0.695 Positive Predictive Value TurboFold(20): 0.919 HotKnots: 0.705 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RNAfold Matthews Correlation Coefficient TurboFold(20): 0.889 RNAfold: 0.686 Sensitivity TurboFold(20): 0.861 RNAfold: 0.681 Positive Predictive Value TurboFold(20): 0.919 RNAfold: 0.695 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RNAshapes Matthews Correlation Coefficient TurboFold(20): 0.889 RNAshapes: 0.693 Sensitivity TurboFold(20): 0.861 RNAshapes: 0.687 Positive Predictive Value TurboFold(20): 0.919 RNAshapes: 0.702 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RNASampler(seed) Matthews Correlation Coefficient TurboFold(20): 0.769 RNASampler(seed): 0.571 Sensitivity TurboFold(20): 0.707 RNASampler(seed): 0.343 Positive Predictive Value TurboFold(20): 0.841 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Afold Matthews Correlation Coefficient TurboFold(20): 0.858 Afold: 0.643 Sensitivity TurboFold(20): 0.826 Afold: 0.632 Positive Predictive Value TurboFold(20): 0.893 Afold: 0.659 Number of pairs reference - predicted secondary structure: 163 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Pknots Matthews Correlation Coefficient TurboFold(20): 0.910 Pknots: 0.655 Sensitivity TurboFold(20): 0.885 Pknots: 0.662 Positive Predictive Value TurboFold(20): 0.937 Pknots: 0.653 Number of pairs reference - predicted secondary structure: 212 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs McQFold Matthews Correlation Coefficient TurboFold(20): 0.889 McQFold: 0.610 Sensitivity TurboFold(20): 0.861 McQFold: 0.587 Positive Predictive Value TurboFold(20): 0.919 McQFold: 0.639 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Carnac(20) Matthews Correlation Coefficient TurboFold(20): 0.889 Carnac(20): 0.675 Sensitivity TurboFold(20): 0.861 Carnac(20): 0.500 Positive Predictive Value TurboFold(20): 0.919 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RNASLOpt Matthews Correlation Coefficient TurboFold(20): 0.889 RNASLOpt: 0.638 Sensitivity TurboFold(20): 0.861 RNASLOpt: 0.594 Positive Predictive Value TurboFold(20): 0.919 RNASLOpt: 0.690 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Cylofold Matthews Correlation Coefficient TurboFold(20): 0.892 Cylofold: 0.557 Sensitivity TurboFold(20): 0.864 Cylofold: 0.543 Positive Predictive Value TurboFold(20): 0.922 Cylofold: 0.577 Number of pairs reference - predicted secondary structure: 304 Wilcoxon single-rank test P-value: 3.56938820447e-08	? TurboFold(20) vs Multilign(seed) Matthews Correlation Coefficient TurboFold(20): 0.571 Multilign(seed): 0.334 Sensitivity TurboFold(20): 0.512 Multilign(seed): 0.186 Positive Predictive Value TurboFold(20): 0.647 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ TurboFold(20) vs RNAwolf Matthews Correlation Coefficient TurboFold(20): 0.889 RNAwolf: 0.561 Sensitivity TurboFold(20): 0.861 RNAwolf: 0.565 Positive Predictive Value TurboFold(20): 0.919 RNAwolf: 0.561 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs PPfold(seed) Matthews Correlation Coefficient TurboFold(20): 0.871 PPfold(seed): 0.344 Sensitivity TurboFold(20): 0.870 PPfold(seed): 0.128 Positive Predictive Value TurboFold(20): 0.873 PPfold(seed): 0.927 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ TurboFold(20) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(20): 0.790 Murlet(seed): 0.636 Sensitivity TurboFold(20): 0.734 Murlet(seed): 0.428 Positive Predictive Value TurboFold(20): 0.855 Murlet(seed): 0.952 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Alterna Matthews Correlation Coefficient TurboFold(20): 0.913 Alterna: 0.618 Sensitivity TurboFold(20): 0.887 Alterna: 0.626 Positive Predictive Value TurboFold(20): 0.940 Alterna: 0.616 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(20): 0.834 Carnac(seed): 0.431 Sensitivity TurboFold(20): 0.797 Carnac(seed): 0.206 Positive Predictive Value TurboFold(20): 0.875 Carnac(seed): 0.907 Number of pairs reference - predicted secondary structure: 68 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Vsfold4 Matthews Correlation Coefficient TurboFold(20): 0.889 Vsfold4: 0.502 Sensitivity TurboFold(20): 0.861 Vsfold4: 0.466 Positive Predictive Value TurboFold(20): 0.919 Vsfold4: 0.546 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(20): 0.830 RSpredict(seed): 0.414 Sensitivity TurboFold(20): 0.812 RSpredict(seed): 0.279 Positive Predictive Value TurboFold(20): 0.850 RSpredict(seed): 0.622 Number of pairs reference - predicted secondary structure: 141 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Vsfold5 Matthews Correlation Coefficient TurboFold(20): 0.889 Vsfold5: 0.457 Sensitivity TurboFold(20): 0.861 Vsfold5: 0.437 Positive Predictive Value TurboFold(20): 0.919 Vsfold5: 0.484 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs RDfolder Matthews Correlation Coefficient TurboFold(20): 0.913 RDfolder: 0.556 Sensitivity TurboFold(20): 0.887 RDfolder: 0.511 Positive Predictive Value TurboFold(20): 0.940 RDfolder: 0.611 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs MCFold Matthews Correlation Coefficient TurboFold(20): 0.885 MCFold: 0.500 Sensitivity TurboFold(20): 0.859 MCFold: 0.559 Positive Predictive Value TurboFold(20): 0.914 MCFold: 0.453 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs NanoFolder Matthews Correlation Coefficient TurboFold(20): 0.888 NanoFolder: 0.337 Sensitivity TurboFold(20): 0.859 NanoFolder: 0.391 Positive Predictive Value TurboFold(20): 0.919 NanoFolder: 0.298 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(20) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(20): 0.839 Mastr(seed): 0.265 Sensitivity TurboFold(20): 0.818 Mastr(seed): 0.087 Positive Predictive Value TurboFold(20): 0.863 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 154 Wilcoxon single-rank test P-value: 3.56938820447e-08
CentroidAlifold(seed)	216 ContextFold vs CentroidAlifold(seed) Matthews Correlation Coefficient ContextFold: 0.839 CentroidAlifold(seed): 0.790 Sensitivity ContextFold: 0.812 CentroidAlifold(seed): 0.699 Positive Predictive Value ContextFold: 0.868 CentroidAlifold(seed): 0.896 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	141 TurboFold(20) vs CentroidAlifold(seed) Matthews Correlation Coefficient TurboFold(20): 0.830 CentroidAlifold(seed): 0.815 Sensitivity TurboFold(20): 0.812 CentroidAlifold(seed): 0.743 Positive Predictive Value TurboFold(20): 0.850 CentroidAlifold(seed): 0.897 Number of pairs reference - predicted secondary structure: 141 Wilcoxon single-rank test P-value: 3.56938820447e-08		- CentroidHomfold‑LAST vs CentroidAlifold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.794 CentroidAlifold(seed): 0.790 Sensitivity CentroidHomfold‑LAST: 0.737 CentroidAlifold(seed): 0.699 Positive Predictive Value CentroidHomfold‑LAST: 0.858 CentroidAlifold(seed): 0.896 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 1.22032703654e-06	+ CentroidAlifold(seed) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.791 PETfold_pre2.0(seed): 0.750 Sensitivity CentroidAlifold(seed): 0.700 PETfold_pre2.0(seed): 0.654 Positive Predictive Value CentroidAlifold(seed): 0.898 PETfold_pre2.0(seed): 0.862 Number of pairs reference - predicted secondary structure: 213 Wilcoxon single-rank test P-value: 3.56938820447e-08	= CentroidAlifold(seed) vs TurboFold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.798 TurboFold(seed): 0.790 Sensitivity CentroidAlifold(seed): 0.694 TurboFold(seed): 0.759 Positive Predictive Value CentroidAlifold(seed): 0.921 TurboFold(seed): 0.826 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 0.00272284868513	+ CentroidAlifold(seed) vs MXScarna(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.790 MXScarna(seed): 0.739 Sensitivity CentroidAlifold(seed): 0.699 MXScarna(seed): 0.701 Positive Predictive Value CentroidAlifold(seed): 0.896 MXScarna(seed): 0.783 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.815 CentroidAlifold(20): 0.702 Sensitivity CentroidAlifold(seed): 0.743 CentroidAlifold(20): 0.525 Positive Predictive Value CentroidAlifold(seed): 0.897 CentroidAlifold(20): 0.944 Number of pairs reference - predicted secondary structure: 141 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.815 PETfold_pre2.0(20): 0.641 Sensitivity CentroidAlifold(seed): 0.743 PETfold_pre2.0(20): 0.440 Positive Predictive Value CentroidAlifold(seed): 0.897 PETfold_pre2.0(20): 0.938 Number of pairs reference - predicted secondary structure: 141 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs MXScarna(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.815 MXScarna(20): 0.764 Sensitivity CentroidAlifold(seed): 0.743 MXScarna(20): 0.686 Positive Predictive Value CentroidAlifold(seed): 0.897 MXScarna(20): 0.854 Number of pairs reference - predicted secondary structure: 141 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs PPfold(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.816 PPfold(20): 0.625 Sensitivity CentroidAlifold(seed): 0.741 PPfold(20): 0.415 Positive Predictive Value CentroidAlifold(seed): 0.900 PPfold(20): 0.944 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNAalifold(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.815 RNAalifold(20): 0.642 Sensitivity CentroidAlifold(seed): 0.743 RNAalifold(20): 0.442 Positive Predictive Value CentroidAlifold(seed): 0.897 RNAalifold(20): 0.937 Number of pairs reference - predicted secondary structure: 141 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.815 RSpredict(20): 0.716 Sensitivity CentroidAlifold(seed): 0.743 RSpredict(20): 0.594 Positive Predictive Value CentroidAlifold(seed): 0.897 RSpredict(20): 0.866 Number of pairs reference - predicted secondary structure: 141 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs IPknot Matthews Correlation Coefficient CentroidAlifold(seed): 0.790 IPknot: 0.733 Sensitivity CentroidAlifold(seed): 0.699 IPknot: 0.708 Positive Predictive Value CentroidAlifold(seed): 0.896 IPknot: 0.762 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.818 Multilign(20): 0.593 Sensitivity CentroidAlifold(seed): 0.744 Multilign(20): 0.447 Positive Predictive Value CentroidAlifold(seed): 0.901 Multilign(20): 0.793 Number of pairs reference - predicted secondary structure: 132 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.790 CentroidFold: 0.699 Sensitivity CentroidAlifold(seed): 0.699 CentroidFold: 0.665 Positive Predictive Value CentroidAlifold(seed): 0.896 CentroidFold: 0.739 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.790 Contrafold: 0.692 Sensitivity CentroidAlifold(seed): 0.699 Contrafold: 0.681 Positive Predictive Value CentroidAlifold(seed): 0.896 Contrafold: 0.707 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNASampler(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.819 RNASampler(20): 0.604 Sensitivity CentroidAlifold(seed): 0.744 RNASampler(20): 0.394 Positive Predictive Value CentroidAlifold(seed): 0.904 RNASampler(20): 0.931 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.816 Murlet(20): 0.609 Sensitivity CentroidAlifold(seed): 0.744 Murlet(20): 0.404 Positive Predictive Value CentroidAlifold(seed): 0.898 Murlet(20): 0.922 Number of pairs reference - predicted secondary structure: 140 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs CMfinder(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.804 CMfinder(seed): 0.571 Sensitivity CentroidAlifold(seed): 0.666 CMfinder(seed): 0.439 Positive Predictive Value CentroidAlifold(seed): 0.974 CMfinder(seed): 0.747 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(seed): 0.790 MaxExpect: 0.694 Sensitivity CentroidAlifold(seed): 0.699 MaxExpect: 0.684 Positive Predictive Value CentroidAlifold(seed): 0.896 MaxExpect: 0.707 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs CMfinder(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.816 CMfinder(20): 0.649 Sensitivity CentroidAlifold(seed): 0.744 CMfinder(20): 0.500 Positive Predictive Value CentroidAlifold(seed): 0.896 CMfinder(20): 0.846 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs CRWrnafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.790 CRWrnafold: 0.705 Sensitivity CentroidAlifold(seed): 0.699 CRWrnafold: 0.696 Positive Predictive Value CentroidAlifold(seed): 0.896 CRWrnafold: 0.716 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(seed): 0.790 ProbKnot: 0.687 Sensitivity CentroidAlifold(seed): 0.699 ProbKnot: 0.680 Positive Predictive Value CentroidAlifold(seed): 0.896 ProbKnot: 0.697 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.815 Mastr(20): 0.659 Sensitivity CentroidAlifold(seed): 0.743 Mastr(20): 0.520 Positive Predictive Value CentroidAlifold(seed): 0.897 Mastr(20): 0.839 Number of pairs reference - predicted secondary structure: 141 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Fold Matthews Correlation Coefficient CentroidAlifold(seed): 0.790 Fold: 0.701 Sensitivity CentroidAlifold(seed): 0.699 Fold: 0.699 Positive Predictive Value CentroidAlifold(seed): 0.896 Fold: 0.706 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.790 UNAFold: 0.702 Sensitivity CentroidAlifold(seed): 0.699 UNAFold: 0.695 Positive Predictive Value CentroidAlifold(seed): 0.896 UNAFold: 0.713 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(seed): 0.790 PknotsRG: 0.705 Sensitivity CentroidAlifold(seed): 0.699 PknotsRG: 0.705 Positive Predictive Value CentroidAlifold(seed): 0.896 PknotsRG: 0.710 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Sfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.790 Sfold: 0.686 Sensitivity CentroidAlifold(seed): 0.699 Sfold: 0.656 Positive Predictive Value CentroidAlifold(seed): 0.896 Sfold: 0.721 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.802 RNAalifold(seed): 0.610 Sensitivity CentroidAlifold(seed): 0.719 RNAalifold(seed): 0.404 Positive Predictive Value CentroidAlifold(seed): 0.896 RNAalifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(seed): 0.790 RNAsubopt: 0.655 Sensitivity CentroidAlifold(seed): 0.699 RNAsubopt: 0.654 Positive Predictive Value CentroidAlifold(seed): 0.896 RNAsubopt: 0.660 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(seed): 0.788 HotKnots: 0.688 Sensitivity CentroidAlifold(seed): 0.697 HotKnots: 0.689 Positive Predictive Value CentroidAlifold(seed): 0.894 HotKnots: 0.691 Number of pairs reference - predicted secondary structure: 212 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.790 RNAfold: 0.694 Sensitivity CentroidAlifold(seed): 0.699 RNAfold: 0.691 Positive Predictive Value CentroidAlifold(seed): 0.896 RNAfold: 0.702 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(seed): 0.790 RNAshapes: 0.680 Sensitivity CentroidAlifold(seed): 0.699 RNAshapes: 0.677 Positive Predictive Value CentroidAlifold(seed): 0.896 RNAshapes: 0.686 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNASampler(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.810 RNASampler(seed): 0.557 Sensitivity CentroidAlifold(seed): 0.674 RNASampler(seed): 0.389 Positive Predictive Value CentroidAlifold(seed): 0.976 RNASampler(seed): 0.802 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Afold Matthews Correlation Coefficient CentroidAlifold(seed): 0.811 Afold: 0.649 Sensitivity CentroidAlifold(seed): 0.727 Afold: 0.646 Positive Predictive Value CentroidAlifold(seed): 0.906 Afold: 0.657 Number of pairs reference - predicted secondary structure: 162 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Pknots Matthews Correlation Coefficient CentroidAlifold(seed): 0.780 Pknots: 0.509 Sensitivity CentroidAlifold(seed): 0.673 Pknots: 0.504 Positive Predictive Value CentroidAlifold(seed): 0.906 Pknots: 0.523 Number of pairs reference - predicted secondary structure: 146 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs McQFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.790 McQFold: 0.562 Sensitivity CentroidAlifold(seed): 0.699 McQFold: 0.537 Positive Predictive Value CentroidAlifold(seed): 0.896 McQFold: 0.593 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.815 Carnac(20): 0.467 Sensitivity CentroidAlifold(seed): 0.743 Carnac(20): 0.260 Positive Predictive Value CentroidAlifold(seed): 0.897 Carnac(20): 0.845 Number of pairs reference - predicted secondary structure: 141 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(seed): 0.790 RNASLOpt: 0.579 Sensitivity CentroidAlifold(seed): 0.699 RNASLOpt: 0.530 Positive Predictive Value CentroidAlifold(seed): 0.896 RNASLOpt: 0.638 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Cylofold Matthews Correlation Coefficient CentroidAlifold(seed): 0.785 Cylofold: 0.518 Sensitivity CentroidAlifold(seed): 0.694 Cylofold: 0.491 Positive Predictive Value CentroidAlifold(seed): 0.892 Cylofold: 0.552 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Multilign(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.683 Multilign(seed): 0.485 Sensitivity CentroidAlifold(seed): 0.516 Multilign(seed): 0.386 Positive Predictive Value CentroidAlifold(seed): 0.910 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.34193807955e-08	+ CentroidAlifold(seed) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(seed): 0.790 RNAwolf: 0.529 Sensitivity CentroidAlifold(seed): 0.699 RNAwolf: 0.534 Positive Predictive Value CentroidAlifold(seed): 0.896 RNAwolf: 0.529 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs PPfold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.740 PPfold(seed): 0.380 Sensitivity CentroidAlifold(seed): 0.602 PPfold(seed): 0.170 Positive Predictive Value CentroidAlifold(seed): 0.912 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.810 Murlet(seed): 0.468 Sensitivity CentroidAlifold(seed): 0.679 Murlet(seed): 0.266 Positive Predictive Value CentroidAlifold(seed): 0.968 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Alterna Matthews Correlation Coefficient CentroidAlifold(seed): 0.781 Alterna: 0.558 Sensitivity CentroidAlifold(seed): 0.674 Alterna: 0.548 Positive Predictive Value CentroidAlifold(seed): 0.908 Alterna: 0.575 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.798 Carnac(seed): 0.424 Sensitivity CentroidAlifold(seed): 0.671 Carnac(seed): 0.205 Positive Predictive Value CentroidAlifold(seed): 0.951 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 120 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(seed): 0.790 Vsfold4: 0.355 Sensitivity CentroidAlifold(seed): 0.699 Vsfold4: 0.324 Positive Predictive Value CentroidAlifold(seed): 0.896 Vsfold4: 0.397 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.790 RSpredict(seed): 0.373 Sensitivity CentroidAlifold(seed): 0.699 RSpredict(seed): 0.251 Positive Predictive Value CentroidAlifold(seed): 0.896 RSpredict(seed): 0.562 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(seed): 0.790 Vsfold5: 0.309 Sensitivity CentroidAlifold(seed): 0.699 Vsfold5: 0.289 Positive Predictive Value CentroidAlifold(seed): 0.896 Vsfold5: 0.338 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.781 RDfolder: 0.468 Sensitivity CentroidAlifold(seed): 0.674 RDfolder: 0.402 Positive Predictive Value CentroidAlifold(seed): 0.908 RDfolder: 0.552 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs MCFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.786 MCFold: 0.472 Sensitivity CentroidAlifold(seed): 0.691 MCFold: 0.523 Positive Predictive Value CentroidAlifold(seed): 0.896 MCFold: 0.432 Number of pairs reference - predicted secondary structure: 185 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.811 NanoFolder: 0.391 Sensitivity CentroidAlifold(seed): 0.730 NanoFolder: 0.446 Positive Predictive Value CentroidAlifold(seed): 0.902 NanoFolder: 0.350 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(seed) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.790 Mastr(seed): 0.276 Sensitivity CentroidAlifold(seed): 0.699 Mastr(seed): 0.097 Positive Predictive Value CentroidAlifold(seed): 0.896 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08
CentroidHomfold‑LAST	882 ContextFold vs CentroidHomfold‑LAST Matthews Correlation Coefficient ContextFold: 0.779 CentroidHomfold‑LAST: 0.736 Sensitivity ContextFold: 0.741 CentroidHomfold‑LAST: 0.665 Positive Predictive Value ContextFold: 0.823 CentroidHomfold‑LAST: 0.818 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 TurboFold(20) vs CentroidHomfold‑LAST Matthews Correlation Coefficient TurboFold(20): 0.889 CentroidHomfold‑LAST: 0.858 Sensitivity TurboFold(20): 0.861 CentroidHomfold‑LAST: 0.821 Positive Predictive Value TurboFold(20): 0.919 CentroidHomfold‑LAST: 0.900 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	216 CentroidHomfold‑LAST vs CentroidAlifold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.794 CentroidAlifold(seed): 0.790 Sensitivity CentroidHomfold‑LAST: 0.737 CentroidAlifold(seed): 0.699 Positive Predictive Value CentroidHomfold‑LAST: 0.858 CentroidAlifold(seed): 0.896 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 1.22032703654e-06		- PETfold_pre2.0(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.879 CentroidHomfold‑LAST: 0.846 Sensitivity PETfold_pre2.0(seed): 0.825 CentroidHomfold‑LAST: 0.803 Positive Predictive Value PETfold_pre2.0(seed): 0.938 CentroidHomfold‑LAST: 0.895 Number of pairs reference - predicted secondary structure: 498 Wilcoxon single-rank test P-value: 3.56938820447e-08	- TurboFold(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient TurboFold(seed): 0.798 CentroidHomfold‑LAST: 0.786 Sensitivity TurboFold(seed): 0.766 CentroidHomfold‑LAST: 0.745 Positive Predictive Value TurboFold(seed): 0.835 CentroidHomfold‑LAST: 0.832 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs MXScarna(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.801 MXScarna(seed): 0.750 Sensitivity CentroidHomfold‑LAST: 0.744 MXScarna(seed): 0.712 Positive Predictive Value CentroidHomfold‑LAST: 0.864 MXScarna(seed): 0.793 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs CentroidAlifold(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.858 CentroidAlifold(20): 0.849 Sensitivity CentroidHomfold‑LAST: 0.821 CentroidAlifold(20): 0.754 Positive Predictive Value CentroidHomfold‑LAST: 0.900 CentroidAlifold(20): 0.957 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs PETfold_pre2.0(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.858 PETfold_pre2.0(20): 0.847 Sensitivity CentroidHomfold‑LAST: 0.821 PETfold_pre2.0(20): 0.737 Positive Predictive Value CentroidHomfold‑LAST: 0.900 PETfold_pre2.0(20): 0.975 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs MXScarna(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.858 MXScarna(20): 0.838 Sensitivity CentroidHomfold‑LAST: 0.821 MXScarna(20): 0.791 Positive Predictive Value CentroidHomfold‑LAST: 0.900 MXScarna(20): 0.891 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs PPfold(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.859 PPfold(20): 0.839 Sensitivity CentroidHomfold‑LAST: 0.821 PPfold(20): 0.721 Positive Predictive Value CentroidHomfold‑LAST: 0.902 PPfold(20): 0.977 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNAalifold(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.858 RNAalifold(20): 0.816 Sensitivity CentroidHomfold‑LAST: 0.821 RNAalifold(20): 0.690 Positive Predictive Value CentroidHomfold‑LAST: 0.900 RNAalifold(20): 0.966 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RSpredict(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.858 RSpredict(20): 0.789 Sensitivity CentroidHomfold‑LAST: 0.821 RSpredict(20): 0.693 Positive Predictive Value CentroidHomfold‑LAST: 0.900 RSpredict(20): 0.901 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs IPknot Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.736 IPknot: 0.694 Sensitivity CentroidHomfold‑LAST: 0.665 IPknot: 0.661 Positive Predictive Value CentroidHomfold‑LAST: 0.818 IPknot: 0.733 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Multilign(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.857 Multilign(20): 0.784 Sensitivity CentroidHomfold‑LAST: 0.820 Multilign(20): 0.697 Positive Predictive Value CentroidHomfold‑LAST: 0.898 Multilign(20): 0.885 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs CentroidFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.736 CentroidFold: 0.645 Sensitivity CentroidHomfold‑LAST: 0.665 CentroidFold: 0.612 Positive Predictive Value CentroidHomfold‑LAST: 0.818 CentroidFold: 0.684 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Contrafold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.736 Contrafold: 0.643 Sensitivity CentroidHomfold‑LAST: 0.665 Contrafold: 0.634 Positive Predictive Value CentroidHomfold‑LAST: 0.818 Contrafold: 0.657 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNASampler(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.859 RNASampler(20): 0.770 Sensitivity CentroidHomfold‑LAST: 0.821 RNASampler(20): 0.622 Positive Predictive Value CentroidHomfold‑LAST: 0.900 RNASampler(20): 0.957 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Murlet(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.859 Murlet(20): 0.750 Sensitivity CentroidHomfold‑LAST: 0.821 Murlet(20): 0.619 Positive Predictive Value CentroidHomfold‑LAST: 0.901 Murlet(20): 0.913 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs CMfinder(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.709 CMfinder(seed): 0.571 Sensitivity CentroidHomfold‑LAST: 0.631 CMfinder(seed): 0.439 Positive Predictive Value CentroidHomfold‑LAST: 0.801 CMfinder(seed): 0.747 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs MaxExpect Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.736 MaxExpect: 0.633 Sensitivity CentroidHomfold‑LAST: 0.665 MaxExpect: 0.617 Positive Predictive Value CentroidHomfold‑LAST: 0.818 MaxExpect: 0.654 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs CMfinder(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.859 CMfinder(20): 0.735 Sensitivity CentroidHomfold‑LAST: 0.822 CMfinder(20): 0.603 Positive Predictive Value CentroidHomfold‑LAST: 0.900 CMfinder(20): 0.899 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs CRWrnafold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.736 CRWrnafold: 0.630 Sensitivity CentroidHomfold‑LAST: 0.665 CRWrnafold: 0.618 Positive Predictive Value CentroidHomfold‑LAST: 0.818 CRWrnafold: 0.648 Number of pairs reference - predicted secondary structure: 881 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs ProbKnot Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.736 ProbKnot: 0.630 Sensitivity CentroidHomfold‑LAST: 0.665 ProbKnot: 0.622 Positive Predictive Value CentroidHomfold‑LAST: 0.818 ProbKnot: 0.644 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Mastr(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.858 Mastr(20): 0.708 Sensitivity CentroidHomfold‑LAST: 0.821 Mastr(20): 0.635 Positive Predictive Value CentroidHomfold‑LAST: 0.900 Mastr(20): 0.793 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Fold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.736 Fold: 0.628 Sensitivity CentroidHomfold‑LAST: 0.665 Fold: 0.620 Positive Predictive Value CentroidHomfold‑LAST: 0.818 Fold: 0.641 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs UNAFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.736 UNAFold: 0.620 Sensitivity CentroidHomfold‑LAST: 0.665 UNAFold: 0.605 Positive Predictive Value CentroidHomfold‑LAST: 0.818 UNAFold: 0.639 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs PknotsRG Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.736 PknotsRG: 0.617 Sensitivity CentroidHomfold‑LAST: 0.665 PknotsRG: 0.610 Positive Predictive Value CentroidHomfold‑LAST: 0.818 PknotsRG: 0.630 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Sfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.736 Sfold: 0.618 Sensitivity CentroidHomfold‑LAST: 0.665 Sfold: 0.581 Positive Predictive Value CentroidHomfold‑LAST: 0.818 Sfold: 0.663 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNAalifold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.793 RNAalifold(seed): 0.610 Sensitivity CentroidHomfold‑LAST: 0.735 RNAalifold(seed): 0.404 Positive Predictive Value CentroidHomfold‑LAST: 0.858 RNAalifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNAsubopt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.736 RNAsubopt: 0.615 Sensitivity CentroidHomfold‑LAST: 0.665 RNAsubopt: 0.609 Positive Predictive Value CentroidHomfold‑LAST: 0.818 RNAsubopt: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs HotKnots Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.735 HotKnots: 0.613 Sensitivity CentroidHomfold‑LAST: 0.666 HotKnots: 0.607 Positive Predictive Value CentroidHomfold‑LAST: 0.816 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 875 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNAfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.736 RNAfold: 0.612 Sensitivity CentroidHomfold‑LAST: 0.665 RNAfold: 0.604 Positive Predictive Value CentroidHomfold‑LAST: 0.818 RNAfold: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNAshapes Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.736 RNAshapes: 0.612 Sensitivity CentroidHomfold‑LAST: 0.665 RNAshapes: 0.602 Positive Predictive Value CentroidHomfold‑LAST: 0.818 RNAshapes: 0.628 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNASampler(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.714 RNASampler(seed): 0.557 Sensitivity CentroidHomfold‑LAST: 0.637 RNASampler(seed): 0.389 Positive Predictive Value CentroidHomfold‑LAST: 0.805 RNASampler(seed): 0.802 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Afold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.676 Afold: 0.558 Sensitivity CentroidHomfold‑LAST: 0.596 Afold: 0.541 Positive Predictive Value CentroidHomfold‑LAST: 0.771 Afold: 0.582 Number of pairs reference - predicted secondary structure: 530 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Pknots Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.745 Pknots: 0.606 Sensitivity CentroidHomfold‑LAST: 0.685 Pknots: 0.595 Positive Predictive Value CentroidHomfold‑LAST: 0.815 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs McQFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.736 McQFold: 0.583 Sensitivity CentroidHomfold‑LAST: 0.665 McQFold: 0.557 Positive Predictive Value CentroidHomfold‑LAST: 0.818 McQFold: 0.616 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Carnac(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.858 Carnac(20): 0.675 Sensitivity CentroidHomfold‑LAST: 0.821 Carnac(20): 0.500 Positive Predictive Value CentroidHomfold‑LAST: 0.900 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RNASLOpt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.736 RNASLOpt: 0.562 Sensitivity CentroidHomfold‑LAST: 0.665 RNASLOpt: 0.521 Positive Predictive Value CentroidHomfold‑LAST: 0.818 RNASLOpt: 0.613 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Cylofold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.765 Cylofold: 0.577 Sensitivity CentroidHomfold‑LAST: 0.707 Cylofold: 0.554 Positive Predictive Value CentroidHomfold‑LAST: 0.832 Cylofold: 0.608 Number of pairs reference - predicted secondary structure: 796 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Multilign(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.597 Multilign(seed): 0.485 Sensitivity CentroidHomfold‑LAST: 0.498 Multilign(seed): 0.386 Positive Predictive Value CentroidHomfold‑LAST: 0.723 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.28439804626e-08	+ CentroidHomfold‑LAST vs RNAwolf Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.736 RNAwolf: 0.518 Sensitivity CentroidHomfold‑LAST: 0.665 RNAwolf: 0.523 Positive Predictive Value CentroidHomfold‑LAST: 0.818 RNAwolf: 0.520 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs PPfold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.794 PPfold(seed): 0.380 Sensitivity CentroidHomfold‑LAST: 0.742 PPfold(seed): 0.170 Positive Predictive Value CentroidHomfold‑LAST: 0.853 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Murlet(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.731 Murlet(seed): 0.468 Sensitivity CentroidHomfold‑LAST: 0.658 Murlet(seed): 0.266 Positive Predictive Value CentroidHomfold‑LAST: 0.814 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Alterna Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.748 Alterna: 0.552 Sensitivity CentroidHomfold‑LAST: 0.687 Alterna: 0.547 Positive Predictive Value CentroidHomfold‑LAST: 0.818 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Carnac(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.765 Carnac(seed): 0.415 Sensitivity CentroidHomfold‑LAST: 0.702 Carnac(seed): 0.196 Positive Predictive Value CentroidHomfold‑LAST: 0.838 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Vsfold4 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.736 Vsfold4: 0.487 Sensitivity CentroidHomfold‑LAST: 0.665 Vsfold4: 0.447 Positive Predictive Value CentroidHomfold‑LAST: 0.818 Vsfold4: 0.537 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RSpredict(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.794 RSpredict(seed): 0.373 Sensitivity CentroidHomfold‑LAST: 0.737 RSpredict(seed): 0.251 Positive Predictive Value CentroidHomfold‑LAST: 0.858 RSpredict(seed): 0.562 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Vsfold5 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.736 Vsfold5: 0.477 Sensitivity CentroidHomfold‑LAST: 0.665 Vsfold5: 0.450 Positive Predictive Value CentroidHomfold‑LAST: 0.818 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs RDfolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.748 RDfolder: 0.520 Sensitivity CentroidHomfold‑LAST: 0.687 RDfolder: 0.464 Positive Predictive Value CentroidHomfold‑LAST: 0.818 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs MCFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.736 MCFold: 0.473 Sensitivity CentroidHomfold‑LAST: 0.671 MCFold: 0.524 Positive Predictive Value CentroidHomfold‑LAST: 0.812 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs NanoFolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.760 NanoFolder: 0.335 Sensitivity CentroidHomfold‑LAST: 0.686 NanoFolder: 0.384 Positive Predictive Value CentroidHomfold‑LAST: 0.844 NanoFolder: 0.301 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidHomfold‑LAST vs Mastr(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.801 Mastr(seed): 0.263 Sensitivity CentroidHomfold‑LAST: 0.744 Mastr(seed): 0.089 Positive Predictive Value CentroidHomfold‑LAST: 0.865 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08
PETfold_pre2.0(seed)	498 ContextFold vs PETfold_pre2.0(seed) Matthews Correlation Coefficient ContextFold: 0.893 PETfold_pre2.0(seed): 0.879 Sensitivity ContextFold: 0.864 PETfold_pre2.0(seed): 0.825 Positive Predictive Value ContextFold: 0.925 PETfold_pre2.0(seed): 0.938 Number of pairs reference - predicted secondary structure: 498 Wilcoxon single-rank test P-value: 3.56938820447e-08	319 TurboFold(20) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient TurboFold(20): 0.890 PETfold_pre2.0(seed): 0.885 Sensitivity TurboFold(20): 0.862 PETfold_pre2.0(seed): 0.832 Positive Predictive Value TurboFold(20): 0.920 PETfold_pre2.0(seed): 0.944 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 7.5939721025e-08	213 CentroidAlifold(seed) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.791 PETfold_pre2.0(seed): 0.750 Sensitivity CentroidAlifold(seed): 0.700 PETfold_pre2.0(seed): 0.654 Positive Predictive Value CentroidAlifold(seed): 0.898 PETfold_pre2.0(seed): 0.862 Number of pairs reference - predicted secondary structure: 213 Wilcoxon single-rank test P-value: 3.56938820447e-08	498 PETfold_pre2.0(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.879 CentroidHomfold‑LAST: 0.846 Sensitivity PETfold_pre2.0(seed): 0.825 CentroidHomfold‑LAST: 0.803 Positive Predictive Value PETfold_pre2.0(seed): 0.938 CentroidHomfold‑LAST: 0.895 Number of pairs reference - predicted secondary structure: 498 Wilcoxon single-rank test P-value: 3.56938820447e-08		- TurboFold(seed) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient TurboFold(seed): 0.807 PETfold_pre2.0(seed): 0.724 Sensitivity TurboFold(seed): 0.770 PETfold_pre2.0(seed): 0.621 Positive Predictive Value TurboFold(seed): 0.849 PETfold_pre2.0(seed): 0.847 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.769 MXScarna(seed): 0.751 Sensitivity PETfold_pre2.0(seed): 0.678 MXScarna(seed): 0.712 Positive Predictive Value PETfold_pre2.0(seed): 0.874 MXScarna(seed): 0.795 Number of pairs reference - predicted secondary structure: 230 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.885 CentroidAlifold(20): 0.849 Sensitivity PETfold_pre2.0(seed): 0.832 CentroidAlifold(20): 0.754 Positive Predictive Value PETfold_pre2.0(seed): 0.944 CentroidAlifold(20): 0.958 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.885 PETfold_pre2.0(20): 0.848 Sensitivity PETfold_pre2.0(seed): 0.832 PETfold_pre2.0(20): 0.739 Positive Predictive Value PETfold_pre2.0(seed): 0.944 PETfold_pre2.0(20): 0.976 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.885 MXScarna(20): 0.839 Sensitivity PETfold_pre2.0(seed): 0.832 MXScarna(20): 0.791 Positive Predictive Value PETfold_pre2.0(seed): 0.944 MXScarna(20): 0.892 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs PPfold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.889 PPfold(20): 0.840 Sensitivity PETfold_pre2.0(seed): 0.837 PPfold(20): 0.723 Positive Predictive Value PETfold_pre2.0(seed): 0.946 PPfold(20): 0.977 Number of pairs reference - predicted secondary structure: 313 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.885 RNAalifold(20): 0.816 Sensitivity PETfold_pre2.0(seed): 0.832 RNAalifold(20): 0.690 Positive Predictive Value PETfold_pre2.0(seed): 0.944 RNAalifold(20): 0.968 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.885 RSpredict(20): 0.789 Sensitivity PETfold_pre2.0(seed): 0.832 RSpredict(20): 0.693 Positive Predictive Value PETfold_pre2.0(seed): 0.944 RSpredict(20): 0.901 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.879 IPknot: 0.761 Sensitivity PETfold_pre2.0(seed): 0.825 IPknot: 0.737 Positive Predictive Value PETfold_pre2.0(seed): 0.938 IPknot: 0.788 Number of pairs reference - predicted secondary structure: 498 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.892 Multilign(20): 0.785 Sensitivity PETfold_pre2.0(seed): 0.841 Multilign(20): 0.697 Positive Predictive Value PETfold_pre2.0(seed): 0.947 Multilign(20): 0.887 Number of pairs reference - predicted secondary structure: 310 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.879 CentroidFold: 0.721 Sensitivity PETfold_pre2.0(seed): 0.825 CentroidFold: 0.691 Positive Predictive Value PETfold_pre2.0(seed): 0.938 CentroidFold: 0.755 Number of pairs reference - predicted secondary structure: 498 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.879 Contrafold: 0.715 Sensitivity PETfold_pre2.0(seed): 0.825 Contrafold: 0.710 Positive Predictive Value PETfold_pre2.0(seed): 0.938 Contrafold: 0.724 Number of pairs reference - predicted secondary structure: 498 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.888 RNASampler(20): 0.771 Sensitivity PETfold_pre2.0(seed): 0.834 RNASampler(20): 0.623 Positive Predictive Value PETfold_pre2.0(seed): 0.946 RNASampler(20): 0.957 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.885 Murlet(20): 0.750 Sensitivity PETfold_pre2.0(seed): 0.832 Murlet(20): 0.619 Positive Predictive Value PETfold_pre2.0(seed): 0.944 Murlet(20): 0.913 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs CMfinder(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.745 CMfinder(seed): 0.571 Sensitivity PETfold_pre2.0(seed): 0.645 CMfinder(seed): 0.439 Positive Predictive Value PETfold_pre2.0(seed): 0.864 CMfinder(seed): 0.747 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.879 MaxExpect: 0.694 Sensitivity PETfold_pre2.0(seed): 0.825 MaxExpect: 0.685 Positive Predictive Value PETfold_pre2.0(seed): 0.938 MaxExpect: 0.706 Number of pairs reference - predicted secondary structure: 498 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.888 CMfinder(20): 0.735 Sensitivity PETfold_pre2.0(seed): 0.837 CMfinder(20): 0.603 Positive Predictive Value PETfold_pre2.0(seed): 0.945 CMfinder(20): 0.899 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs CRWrnafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.879 CRWrnafold: 0.718 Sensitivity PETfold_pre2.0(seed): 0.825 CRWrnafold: 0.713 Positive Predictive Value PETfold_pre2.0(seed): 0.938 CRWrnafold: 0.725 Number of pairs reference - predicted secondary structure: 498 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.879 ProbKnot: 0.690 Sensitivity PETfold_pre2.0(seed): 0.825 ProbKnot: 0.692 Positive Predictive Value PETfold_pre2.0(seed): 0.938 ProbKnot: 0.692 Number of pairs reference - predicted secondary structure: 498 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.885 Mastr(20): 0.710 Sensitivity PETfold_pre2.0(seed): 0.832 Mastr(20): 0.638 Positive Predictive Value PETfold_pre2.0(seed): 0.944 Mastr(20): 0.793 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.879 Fold: 0.686 Sensitivity PETfold_pre2.0(seed): 0.825 Fold: 0.687 Positive Predictive Value PETfold_pre2.0(seed): 0.938 Fold: 0.689 Number of pairs reference - predicted secondary structure: 498 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.879 UNAFold: 0.670 Sensitivity PETfold_pre2.0(seed): 0.825 UNAFold: 0.665 Positive Predictive Value PETfold_pre2.0(seed): 0.938 UNAFold: 0.680 Number of pairs reference - predicted secondary structure: 498 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.879 PknotsRG: 0.670 Sensitivity PETfold_pre2.0(seed): 0.825 PknotsRG: 0.671 Positive Predictive Value PETfold_pre2.0(seed): 0.938 PknotsRG: 0.673 Number of pairs reference - predicted secondary structure: 498 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.879 Sfold: 0.667 Sensitivity PETfold_pre2.0(seed): 0.825 Sfold: 0.635 Positive Predictive Value PETfold_pre2.0(seed): 0.938 Sfold: 0.705 Number of pairs reference - predicted secondary structure: 498 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RNAalifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.737 RNAalifold(seed): 0.607 Sensitivity PETfold_pre2.0(seed): 0.639 RNAalifold(seed): 0.399 Positive Predictive Value PETfold_pre2.0(seed): 0.854 RNAalifold(seed): 0.927 Number of pairs reference - predicted secondary structure: 202 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.879 RNAsubopt: 0.667 Sensitivity PETfold_pre2.0(seed): 0.825 RNAsubopt: 0.670 Positive Predictive Value PETfold_pre2.0(seed): 0.938 RNAsubopt: 0.668 Number of pairs reference - predicted secondary structure: 498 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs HotKnots Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.879 HotKnots: 0.657 Sensitivity PETfold_pre2.0(seed): 0.826 HotKnots: 0.660 Positive Predictive Value PETfold_pre2.0(seed): 0.938 HotKnots: 0.659 Number of pairs reference - predicted secondary structure: 494 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.879 RNAfold: 0.659 Sensitivity PETfold_pre2.0(seed): 0.825 RNAfold: 0.659 Positive Predictive Value PETfold_pre2.0(seed): 0.938 RNAfold: 0.663 Number of pairs reference - predicted secondary structure: 498 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.879 RNAshapes: 0.659 Sensitivity PETfold_pre2.0(seed): 0.825 RNAshapes: 0.659 Positive Predictive Value PETfold_pre2.0(seed): 0.938 RNAshapes: 0.664 Number of pairs reference - predicted secondary structure: 498 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RNASampler(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.749 RNASampler(seed): 0.557 Sensitivity PETfold_pre2.0(seed): 0.650 RNASampler(seed): 0.389 Positive Predictive Value PETfold_pre2.0(seed): 0.866 RNASampler(seed): 0.802 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.825 Afold: 0.627 Sensitivity PETfold_pre2.0(seed): 0.751 Afold: 0.616 Positive Predictive Value PETfold_pre2.0(seed): 0.908 Afold: 0.642 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Pknots Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.909 Pknots: 0.666 Sensitivity PETfold_pre2.0(seed): 0.870 Pknots: 0.673 Positive Predictive Value PETfold_pre2.0(seed): 0.950 Pknots: 0.663 Number of pairs reference - predicted secondary structure: 360 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.879 McQFold: 0.635 Sensitivity PETfold_pre2.0(seed): 0.825 McQFold: 0.613 Positive Predictive Value PETfold_pre2.0(seed): 0.938 McQFold: 0.662 Number of pairs reference - predicted secondary structure: 498 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.885 Carnac(20): 0.676 Sensitivity PETfold_pre2.0(seed): 0.832 Carnac(20): 0.501 Positive Predictive Value PETfold_pre2.0(seed): 0.944 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.879 RNASLOpt: 0.630 Sensitivity PETfold_pre2.0(seed): 0.825 RNASLOpt: 0.590 Positive Predictive Value PETfold_pre2.0(seed): 0.938 RNASLOpt: 0.678 Number of pairs reference - predicted secondary structure: 498 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Cylofold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.881 Cylofold: 0.580 Sensitivity PETfold_pre2.0(seed): 0.828 Cylofold: 0.568 Positive Predictive Value PETfold_pre2.0(seed): 0.938 Cylofold: 0.598 Number of pairs reference - predicted secondary structure: 464 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Multilign(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.595 Multilign(seed): 0.485 Sensitivity PETfold_pre2.0(seed): 0.498 Multilign(seed): 0.386 Positive Predictive Value PETfold_pre2.0(seed): 0.718 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.12160100812e-08	+ PETfold_pre2.0(seed) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.879 RNAwolf: 0.535 Sensitivity PETfold_pre2.0(seed): 0.825 RNAwolf: 0.545 Positive Predictive Value PETfold_pre2.0(seed): 0.938 RNAwolf: 0.532 Number of pairs reference - predicted secondary structure: 498 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs PPfold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.765 PPfold(seed): 0.386 Sensitivity PETfold_pre2.0(seed): 0.665 PPfold(seed): 0.176 Positive Predictive Value PETfold_pre2.0(seed): 0.883 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Murlet(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.743 Murlet(seed): 0.468 Sensitivity PETfold_pre2.0(seed): 0.641 Murlet(seed): 0.266 Positive Predictive Value PETfold_pre2.0(seed): 0.863 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Alterna Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.909 Alterna: 0.585 Sensitivity PETfold_pre2.0(seed): 0.870 Alterna: 0.595 Positive Predictive Value PETfold_pre2.0(seed): 0.950 Alterna: 0.582 Number of pairs reference - predicted secondary structure: 360 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.772 Carnac(seed): 0.417 Sensitivity PETfold_pre2.0(seed): 0.676 Carnac(seed): 0.198 Positive Predictive Value PETfold_pre2.0(seed): 0.885 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 122 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.879 Vsfold4: 0.531 Sensitivity PETfold_pre2.0(seed): 0.825 Vsfold4: 0.496 Positive Predictive Value PETfold_pre2.0(seed): 0.938 Vsfold4: 0.575 Number of pairs reference - predicted secondary structure: 498 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.750 RSpredict(seed): 0.367 Sensitivity PETfold_pre2.0(seed): 0.654 RSpredict(seed): 0.245 Positive Predictive Value PETfold_pre2.0(seed): 0.862 RSpredict(seed): 0.557 Number of pairs reference - predicted secondary structure: 213 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.879 Vsfold5: 0.489 Sensitivity PETfold_pre2.0(seed): 0.825 Vsfold5: 0.472 Positive Predictive Value PETfold_pre2.0(seed): 0.938 Vsfold5: 0.514 Number of pairs reference - predicted secondary structure: 498 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs RDfolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.909 RDfolder: 0.557 Sensitivity PETfold_pre2.0(seed): 0.870 RDfolder: 0.511 Positive Predictive Value PETfold_pre2.0(seed): 0.950 RDfolder: 0.615 Number of pairs reference - predicted secondary structure: 360 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.880 MCFold: 0.480 Sensitivity PETfold_pre2.0(seed): 0.828 MCFold: 0.542 Positive Predictive Value PETfold_pre2.0(seed): 0.938 MCFold: 0.431 Number of pairs reference - predicted secondary structure: 407 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.849 NanoFolder: 0.355 Sensitivity PETfold_pre2.0(seed): 0.777 NanoFolder: 0.415 Positive Predictive Value PETfold_pre2.0(seed): 0.929 NanoFolder: 0.312 Number of pairs reference - predicted secondary structure: 79 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(seed) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.769 Mastr(seed): 0.266 Sensitivity PETfold_pre2.0(seed): 0.679 Mastr(seed): 0.090 Positive Predictive Value PETfold_pre2.0(seed): 0.874 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 231 Wilcoxon single-rank test P-value: 3.56938820447e-08
TurboFold(seed)	33 ContextFold vs TurboFold(seed) Matthews Correlation Coefficient ContextFold: 0.822 TurboFold(seed): 0.798 Sensitivity ContextFold: 0.791 TurboFold(seed): 0.766 Positive Predictive Value ContextFold: 0.856 TurboFold(seed): 0.835 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 TurboFold(20) vs TurboFold(seed) Matthews Correlation Coefficient TurboFold(20): 0.885 TurboFold(seed): 0.880 Sensitivity TurboFold(20): 0.880 TurboFold(seed): 0.875 Positive Predictive Value TurboFold(20): 0.891 TurboFold(seed): 0.886 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.70887622364e-08	32 CentroidAlifold(seed) vs TurboFold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.798 TurboFold(seed): 0.790 Sensitivity CentroidAlifold(seed): 0.694 TurboFold(seed): 0.759 Positive Predictive Value CentroidAlifold(seed): 0.921 TurboFold(seed): 0.826 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 0.00272284868513	33 TurboFold(seed) vs CentroidHomfold‑LAST Matthews Correlation Coefficient TurboFold(seed): 0.798 CentroidHomfold‑LAST: 0.786 Sensitivity TurboFold(seed): 0.766 CentroidHomfold‑LAST: 0.745 Positive Predictive Value TurboFold(seed): 0.835 CentroidHomfold‑LAST: 0.832 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	32 TurboFold(seed) vs PETfold_pre2.0(seed) Matthews Correlation Coefficient TurboFold(seed): 0.807 PETfold_pre2.0(seed): 0.724 Sensitivity TurboFold(seed): 0.770 PETfold_pre2.0(seed): 0.621 Positive Predictive Value TurboFold(seed): 0.849 PETfold_pre2.0(seed): 0.847 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ TurboFold(seed) vs MXScarna(seed) Matthews Correlation Coefficient TurboFold(seed): 0.798 MXScarna(seed): 0.728 Sensitivity TurboFold(seed): 0.766 MXScarna(seed): 0.710 Positive Predictive Value TurboFold(seed): 0.835 MXScarna(seed): 0.751 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient TurboFold(seed): 0.880 CentroidAlifold(20): 0.703 Sensitivity TurboFold(seed): 0.875 CentroidAlifold(20): 0.534 Positive Predictive Value TurboFold(seed): 0.886 CentroidAlifold(20): 0.928 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.74172190343e-08	+ TurboFold(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient TurboFold(seed): 0.880 PETfold_pre2.0(20): 0.648 Sensitivity TurboFold(seed): 0.875 PETfold_pre2.0(20): 0.451 Positive Predictive Value TurboFold(seed): 0.886 PETfold_pre2.0(20): 0.934 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.62913390836e-08	+ TurboFold(seed) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(seed): 0.880 MXScarna(20): 0.864 Sensitivity TurboFold(seed): 0.875 MXScarna(20): 0.836 Positive Predictive Value TurboFold(seed): 0.886 MXScarna(20): 0.895 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.32883086441e-08	+ TurboFold(seed) vs PPfold(20) Matthews Correlation Coefficient TurboFold(seed): 0.880 PPfold(20): 0.629 Sensitivity TurboFold(seed): 0.875 PPfold(20): 0.417 Positive Predictive Value TurboFold(seed): 0.886 PPfold(20): 0.955 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.97012568641e-08	+ TurboFold(seed) vs RNAalifold(20) Matthews Correlation Coefficient TurboFold(seed): 0.880 RNAalifold(20): 0.650 Sensitivity TurboFold(seed): 0.875 RNAalifold(20): 0.461 Positive Predictive Value TurboFold(seed): 0.886 RNAalifold(20): 0.922 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.70887622364e-08	+ TurboFold(seed) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(seed): 0.880 RSpredict(20): 0.788 Sensitivity TurboFold(seed): 0.875 RSpredict(20): 0.679 Positive Predictive Value TurboFold(seed): 0.886 RSpredict(20): 0.917 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.76499031155e-08	+ TurboFold(seed) vs IPknot Matthews Correlation Coefficient TurboFold(seed): 0.798 IPknot: 0.781 Sensitivity TurboFold(seed): 0.766 IPknot: 0.756 Positive Predictive Value TurboFold(seed): 0.835 IPknot: 0.811 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs Multilign(20) Matthews Correlation Coefficient TurboFold(seed): 0.877 Multilign(20): 0.574 Sensitivity TurboFold(seed): 0.871 Multilign(20): 0.422 Positive Predictive Value TurboFold(seed): 0.885 Multilign(20): 0.785 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.98760236454e-08	+ TurboFold(seed) vs CentroidFold Matthews Correlation Coefficient TurboFold(seed): 0.798 CentroidFold: 0.762 Sensitivity TurboFold(seed): 0.766 CentroidFold: 0.735 Positive Predictive Value TurboFold(seed): 0.835 CentroidFold: 0.794 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs Contrafold Matthews Correlation Coefficient TurboFold(seed): 0.798 Contrafold: 0.757 Sensitivity TurboFold(seed): 0.766 Contrafold: 0.741 Positive Predictive Value TurboFold(seed): 0.835 Contrafold: 0.778 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs RNASampler(20) Matthews Correlation Coefficient TurboFold(seed): 0.880 RNASampler(20): 0.616 Sensitivity TurboFold(seed): 0.875 RNASampler(20): 0.402 Positive Predictive Value TurboFold(seed): 0.886 RNASampler(20): 0.948 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.1413769576e-08	+ TurboFold(seed) vs Murlet(20) Matthews Correlation Coefficient TurboFold(seed): 0.902 Murlet(20): 0.628 Sensitivity TurboFold(seed): 0.892 Murlet(20): 0.414 Positive Predictive Value TurboFold(seed): 0.914 Murlet(20): 0.957 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.89169006118e-08	= CMfinder(seed) vs TurboFold(seed) Matthews Correlation Coefficient CMfinder(seed): 0.616 TurboFold(seed): 0.607 Sensitivity CMfinder(seed): 0.481 TurboFold(seed): 0.540 Positive Predictive Value CMfinder(seed): 0.796 TurboFold(seed): 0.690 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.00165341959409	+ TurboFold(seed) vs MaxExpect Matthews Correlation Coefficient TurboFold(seed): 0.798 MaxExpect: 0.762 Sensitivity TurboFold(seed): 0.766 MaxExpect: 0.750 Positive Predictive Value TurboFold(seed): 0.835 MaxExpect: 0.778 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs CMfinder(20) Matthews Correlation Coefficient TurboFold(seed): 0.880 CMfinder(20): 0.693 Sensitivity TurboFold(seed): 0.875 CMfinder(20): 0.551 Positive Predictive Value TurboFold(seed): 0.886 CMfinder(20): 0.875 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.80908287419e-08	+ TurboFold(seed) vs CRWrnafold Matthews Correlation Coefficient TurboFold(seed): 0.798 CRWrnafold: 0.724 Sensitivity TurboFold(seed): 0.766 CRWrnafold: 0.715 Positive Predictive Value TurboFold(seed): 0.835 CRWrnafold: 0.736 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs ProbKnot Matthews Correlation Coefficient TurboFold(seed): 0.798 ProbKnot: 0.750 Sensitivity TurboFold(seed): 0.766 ProbKnot: 0.735 Positive Predictive Value TurboFold(seed): 0.835 ProbKnot: 0.769 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ TurboFold(seed) vs Mastr(20) Matthews Correlation Coefficient TurboFold(seed): 0.880 Mastr(20): 0.720 Sensitivity TurboFold(seed): 0.875 Mastr(20): 0.559 Positive Predictive Value TurboFold(seed): 0.886 Mastr(20): 0.931 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 9.54892753461e-09	+ TurboFold(seed) vs Fold Matthews Correlation Coefficient TurboFold(seed): 0.798 Fold: 0.746 Sensitivity TurboFold(seed): 0.766 Fold: 0.739 Positive Predictive Value TurboFold(seed): 0.835 Fold: 0.756 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs UNAFold Matthews Correlation Coefficient TurboFold(seed): 0.798 UNAFold: 0.733 Sensitivity TurboFold(seed): 0.766 UNAFold: 0.719 Positive Predictive Value TurboFold(seed): 0.835 UNAFold: 0.751 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	- PknotsRG vs TurboFold(seed) Matthews Correlation Coefficient PknotsRG: 0.830 TurboFold(seed): 0.798 Sensitivity PknotsRG: 0.826 TurboFold(seed): 0.766 Positive Predictive Value PknotsRG: 0.837 TurboFold(seed): 0.835 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs Sfold Matthews Correlation Coefficient TurboFold(seed): 0.798 Sfold: 0.725 Sensitivity TurboFold(seed): 0.766 Sfold: 0.705 Positive Predictive Value TurboFold(seed): 0.835 Sfold: 0.750 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs RNAalifold(seed) Matthews Correlation Coefficient TurboFold(seed): 0.790 RNAalifold(seed): 0.601 Sensitivity TurboFold(seed): 0.759 RNAalifold(seed): 0.408 Positive Predictive Value TurboFold(seed): 0.826 RNAalifold(seed): 0.890 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs RNAsubopt Matthews Correlation Coefficient TurboFold(seed): 0.798 RNAsubopt: 0.730 Sensitivity TurboFold(seed): 0.766 RNAsubopt: 0.721 Positive Predictive Value TurboFold(seed): 0.835 RNAsubopt: 0.744 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs HotKnots Matthews Correlation Coefficient TurboFold(seed): 0.798 HotKnots: 0.740 Sensitivity TurboFold(seed): 0.766 HotKnots: 0.745 Positive Predictive Value TurboFold(seed): 0.835 HotKnots: 0.740 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ TurboFold(seed) vs RNAfold Matthews Correlation Coefficient TurboFold(seed): 0.798 RNAfold: 0.722 Sensitivity TurboFold(seed): 0.766 RNAfold: 0.714 Positive Predictive Value TurboFold(seed): 0.835 RNAfold: 0.734 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs RNAshapes Matthews Correlation Coefficient TurboFold(seed): 0.798 RNAshapes: 0.726 Sensitivity TurboFold(seed): 0.766 RNAshapes: 0.717 Positive Predictive Value TurboFold(seed): 0.835 RNAshapes: 0.740 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs RNASampler(seed) Matthews Correlation Coefficient TurboFold(seed): 0.697 RNASampler(seed): 0.561 Sensitivity TurboFold(seed): 0.626 RNASampler(seed): 0.414 Positive Predictive Value TurboFold(seed): 0.780 RNASampler(seed): 0.765 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 4.94031556815e-08	+ TurboFold(seed) vs Afold Matthews Correlation Coefficient TurboFold(seed): 0.797 Afold: 0.671 Sensitivity TurboFold(seed): 0.758 Afold: 0.657 Positive Predictive Value TurboFold(seed): 0.841 Afold: 0.689 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ TurboFold(seed) vs Pknots Matthews Correlation Coefficient TurboFold(seed): 0.711 Pknots: 0.628 Sensitivity TurboFold(seed): 0.662 Pknots: 0.632 Positive Predictive Value TurboFold(seed): 0.768 Pknots: 0.630 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ TurboFold(seed) vs McQFold Matthews Correlation Coefficient TurboFold(seed): 0.798 McQFold: 0.623 Sensitivity TurboFold(seed): 0.766 McQFold: 0.600 Positive Predictive Value TurboFold(seed): 0.835 McQFold: 0.652 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs Carnac(20) Matthews Correlation Coefficient TurboFold(seed): 0.880 Carnac(20): 0.511 Sensitivity TurboFold(seed): 0.875 Carnac(20): 0.314 Positive Predictive Value TurboFold(seed): 0.886 Carnac(20): 0.837 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.87872347734e-08	+ TurboFold(seed) vs RNASLOpt Matthews Correlation Coefficient TurboFold(seed): 0.798 RNASLOpt: 0.636 Sensitivity TurboFold(seed): 0.766 RNASLOpt: 0.571 Positive Predictive Value TurboFold(seed): 0.835 RNASLOpt: 0.714 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs Cylofold Matthews Correlation Coefficient TurboFold(seed): 0.800 Cylofold: 0.653 Sensitivity TurboFold(seed): 0.770 Cylofold: 0.626 Positive Predictive Value TurboFold(seed): 0.833 Cylofold: 0.686 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs Multilign(seed) Matthews Correlation Coefficient TurboFold(seed): 0.597 Multilign(seed): 0.485 Sensitivity TurboFold(seed): 0.498 Multilign(seed): 0.386 Positive Predictive Value TurboFold(seed): 0.723 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.00627773251e-08	+ TurboFold(seed) vs RNAwolf Matthews Correlation Coefficient TurboFold(seed): 0.798 RNAwolf: 0.532 Sensitivity TurboFold(seed): 0.766 RNAwolf: 0.527 Positive Predictive Value TurboFold(seed): 0.835 RNAwolf: 0.543 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs PPfold(seed) Matthews Correlation Coefficient TurboFold(seed): 0.778 PPfold(seed): 0.524 Sensitivity TurboFold(seed): 0.727 PPfold(seed): 0.325 Positive Predictive Value TurboFold(seed): 0.837 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 4.50425137787e-08	+ TurboFold(seed) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(seed): 0.755 Murlet(seed): 0.468 Sensitivity TurboFold(seed): 0.706 Murlet(seed): 0.269 Positive Predictive Value TurboFold(seed): 0.812 Murlet(seed): 0.819 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ TurboFold(seed) vs Alterna Matthews Correlation Coefficient TurboFold(seed): 0.720 Alterna: 0.546 Sensitivity TurboFold(seed): 0.663 Alterna: 0.520 Positive Predictive Value TurboFold(seed): 0.786 Alterna: 0.581 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ TurboFold(seed) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(seed): 0.790 Carnac(seed): 0.422 Sensitivity TurboFold(seed): 0.759 Carnac(seed): 0.188 Positive Predictive Value TurboFold(seed): 0.826 Carnac(seed): 0.955 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs Vsfold4 Matthews Correlation Coefficient TurboFold(seed): 0.798 Vsfold4: 0.292 Sensitivity TurboFold(seed): 0.766 Vsfold4: 0.264 Positive Predictive Value TurboFold(seed): 0.835 Vsfold4: 0.334 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(seed): 0.790 RSpredict(seed): 0.462 Sensitivity TurboFold(seed): 0.759 RSpredict(seed): 0.355 Positive Predictive Value TurboFold(seed): 0.826 RSpredict(seed): 0.608 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs Vsfold5 Matthews Correlation Coefficient TurboFold(seed): 0.798 Vsfold5: 0.295 Sensitivity TurboFold(seed): 0.766 Vsfold5: 0.266 Positive Predictive Value TurboFold(seed): 0.835 Vsfold5: 0.337 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs RDfolder Matthews Correlation Coefficient TurboFold(seed): 0.720 RDfolder: 0.512 Sensitivity TurboFold(seed): 0.663 RDfolder: 0.453 Positive Predictive Value TurboFold(seed): 0.786 RDfolder: 0.588 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ TurboFold(seed) vs MCFold Matthews Correlation Coefficient TurboFold(seed): 0.788 MCFold: 0.459 Sensitivity TurboFold(seed): 0.752 MCFold: 0.515 Positive Predictive Value TurboFold(seed): 0.828 MCFold: 0.417 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ TurboFold(seed) vs NanoFolder Matthews Correlation Coefficient TurboFold(seed): 0.834 NanoFolder: 0.423 Sensitivity TurboFold(seed): 0.785 NanoFolder: 0.480 Positive Predictive Value TurboFold(seed): 0.889 NanoFolder: 0.381 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.43692248862e-08	+ TurboFold(seed) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(seed): 0.798 Mastr(seed): 0.330 Sensitivity TurboFold(seed): 0.766 Mastr(seed): 0.154 Positive Predictive Value TurboFold(seed): 0.835 Mastr(seed): 0.714 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08
MXScarna(seed)	233 ContextFold vs MXScarna(seed) Matthews Correlation Coefficient ContextFold: 0.843 MXScarna(seed): 0.750 Sensitivity ContextFold: 0.816 MXScarna(seed): 0.712 Positive Predictive Value ContextFold: 0.873 MXScarna(seed): 0.793 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	153 TurboFold(20) vs MXScarna(seed) Matthews Correlation Coefficient TurboFold(20): 0.839 MXScarna(seed): 0.792 Sensitivity TurboFold(20): 0.818 MXScarna(seed): 0.756 Positive Predictive Value TurboFold(20): 0.862 MXScarna(seed): 0.832 Number of pairs reference - predicted secondary structure: 153 Wilcoxon single-rank test P-value: 3.56938820447e-08	216 CentroidAlifold(seed) vs MXScarna(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.790 MXScarna(seed): 0.739 Sensitivity CentroidAlifold(seed): 0.699 MXScarna(seed): 0.701 Positive Predictive Value CentroidAlifold(seed): 0.896 MXScarna(seed): 0.783 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	233 CentroidHomfold‑LAST vs MXScarna(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.801 MXScarna(seed): 0.750 Sensitivity CentroidHomfold‑LAST: 0.744 MXScarna(seed): 0.712 Positive Predictive Value CentroidHomfold‑LAST: 0.864 MXScarna(seed): 0.793 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	230 PETfold_pre2.0(seed) vs MXScarna(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.769 MXScarna(seed): 0.751 Sensitivity PETfold_pre2.0(seed): 0.678 MXScarna(seed): 0.712 Positive Predictive Value PETfold_pre2.0(seed): 0.874 MXScarna(seed): 0.795 Number of pairs reference - predicted secondary structure: 230 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 TurboFold(seed) vs MXScarna(seed) Matthews Correlation Coefficient TurboFold(seed): 0.798 MXScarna(seed): 0.728 Sensitivity TurboFold(seed): 0.766 MXScarna(seed): 0.710 Positive Predictive Value TurboFold(seed): 0.835 MXScarna(seed): 0.751 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ MXScarna(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient MXScarna(seed): 0.792 CentroidAlifold(20): 0.725 Sensitivity MXScarna(seed): 0.756 CentroidAlifold(20): 0.558 Positive Predictive Value MXScarna(seed): 0.832 CentroidAlifold(20): 0.946 Number of pairs reference - predicted secondary structure: 153 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient MXScarna(seed): 0.792 PETfold_pre2.0(20): 0.674 Sensitivity MXScarna(seed): 0.756 PETfold_pre2.0(20): 0.483 Positive Predictive Value MXScarna(seed): 0.832 PETfold_pre2.0(20): 0.943 Number of pairs reference - predicted secondary structure: 153 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs MXScarna(20) Matthews Correlation Coefficient MXScarna(seed): 0.792 MXScarna(20): 0.778 Sensitivity MXScarna(seed): 0.756 MXScarna(20): 0.705 Positive Predictive Value MXScarna(seed): 0.832 MXScarna(20): 0.863 Number of pairs reference - predicted secondary structure: 153 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs PPfold(20) Matthews Correlation Coefficient MXScarna(seed): 0.795 PPfold(20): 0.659 Sensitivity MXScarna(seed): 0.758 PPfold(20): 0.461 Positive Predictive Value MXScarna(seed): 0.837 PPfold(20): 0.948 Number of pairs reference - predicted secondary structure: 147 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNAalifold(20) Matthews Correlation Coefficient MXScarna(seed): 0.792 RNAalifold(20): 0.669 Sensitivity MXScarna(seed): 0.756 RNAalifold(20): 0.476 Positive Predictive Value MXScarna(seed): 0.832 RNAalifold(20): 0.943 Number of pairs reference - predicted secondary structure: 153 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(seed): 0.792 RSpredict(20): 0.726 Sensitivity MXScarna(seed): 0.756 RSpredict(20): 0.606 Positive Predictive Value MXScarna(seed): 0.832 RSpredict(20): 0.873 Number of pairs reference - predicted secondary structure: 153 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs IPknot Matthews Correlation Coefficient MXScarna(seed): 0.750 IPknot: 0.735 Sensitivity MXScarna(seed): 0.712 IPknot: 0.710 Positive Predictive Value MXScarna(seed): 0.793 IPknot: 0.764 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Multilign(20) Matthews Correlation Coefficient MXScarna(seed): 0.792 Multilign(20): 0.623 Sensitivity MXScarna(seed): 0.757 Multilign(20): 0.481 Positive Predictive Value MXScarna(seed): 0.831 Multilign(20): 0.812 Number of pairs reference - predicted secondary structure: 144 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs CentroidFold Matthews Correlation Coefficient MXScarna(seed): 0.750 CentroidFold: 0.699 Sensitivity MXScarna(seed): 0.712 CentroidFold: 0.665 Positive Predictive Value MXScarna(seed): 0.793 CentroidFold: 0.738 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Contrafold Matthews Correlation Coefficient MXScarna(seed): 0.750 Contrafold: 0.693 Sensitivity MXScarna(seed): 0.712 Contrafold: 0.682 Positive Predictive Value MXScarna(seed): 0.793 Contrafold: 0.707 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNASampler(20) Matthews Correlation Coefficient MXScarna(seed): 0.798 RNASampler(20): 0.632 Sensitivity MXScarna(seed): 0.761 RNASampler(20): 0.427 Positive Predictive Value MXScarna(seed): 0.839 RNASampler(20): 0.939 Number of pairs reference - predicted secondary structure: 149 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Murlet(20) Matthews Correlation Coefficient MXScarna(seed): 0.793 Murlet(20): 0.625 Sensitivity MXScarna(seed): 0.756 Murlet(20): 0.428 Positive Predictive Value MXScarna(seed): 0.834 Murlet(20): 0.918 Number of pairs reference - predicted secondary structure: 152 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs CMfinder(seed) Matthews Correlation Coefficient MXScarna(seed): 0.699 CMfinder(seed): 0.571 Sensitivity MXScarna(seed): 0.663 CMfinder(seed): 0.439 Positive Predictive Value MXScarna(seed): 0.741 CMfinder(seed): 0.747 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs MaxExpect Matthews Correlation Coefficient MXScarna(seed): 0.750 MaxExpect: 0.691 Sensitivity MXScarna(seed): 0.712 MaxExpect: 0.680 Positive Predictive Value MXScarna(seed): 0.793 MaxExpect: 0.705 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(seed): 0.795 CMfinder(20): 0.664 Sensitivity MXScarna(seed): 0.760 CMfinder(20): 0.517 Positive Predictive Value MXScarna(seed): 0.834 CMfinder(20): 0.857 Number of pairs reference - predicted secondary structure: 149 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs CRWrnafold Matthews Correlation Coefficient MXScarna(seed): 0.750 CRWrnafold: 0.701 Sensitivity MXScarna(seed): 0.712 CRWrnafold: 0.693 Positive Predictive Value MXScarna(seed): 0.793 CRWrnafold: 0.713 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs ProbKnot Matthews Correlation Coefficient MXScarna(seed): 0.750 ProbKnot: 0.684 Sensitivity MXScarna(seed): 0.712 ProbKnot: 0.678 Positive Predictive Value MXScarna(seed): 0.793 ProbKnot: 0.694 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Mastr(20) Matthews Correlation Coefficient MXScarna(seed): 0.792 Mastr(20): 0.678 Sensitivity MXScarna(seed): 0.756 Mastr(20): 0.547 Positive Predictive Value MXScarna(seed): 0.832 Mastr(20): 0.843 Number of pairs reference - predicted secondary structure: 153 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Fold Matthews Correlation Coefficient MXScarna(seed): 0.750 Fold: 0.692 Sensitivity MXScarna(seed): 0.712 Fold: 0.690 Positive Predictive Value MXScarna(seed): 0.793 Fold: 0.697 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs UNAFold Matthews Correlation Coefficient MXScarna(seed): 0.750 UNAFold: 0.689 Sensitivity MXScarna(seed): 0.712 UNAFold: 0.683 Positive Predictive Value MXScarna(seed): 0.793 UNAFold: 0.699 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs PknotsRG Matthews Correlation Coefficient MXScarna(seed): 0.750 PknotsRG: 0.693 Sensitivity MXScarna(seed): 0.712 PknotsRG: 0.692 Positive Predictive Value MXScarna(seed): 0.793 PknotsRG: 0.697 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Sfold Matthews Correlation Coefficient MXScarna(seed): 0.750 Sfold: 0.680 Sensitivity MXScarna(seed): 0.712 Sfold: 0.648 Positive Predictive Value MXScarna(seed): 0.793 Sfold: 0.718 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNAalifold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.736 RNAalifold(seed): 0.610 Sensitivity MXScarna(seed): 0.697 RNAalifold(seed): 0.404 Positive Predictive Value MXScarna(seed): 0.780 RNAalifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNAsubopt Matthews Correlation Coefficient MXScarna(seed): 0.750 RNAsubopt: 0.652 Sensitivity MXScarna(seed): 0.712 RNAsubopt: 0.651 Positive Predictive Value MXScarna(seed): 0.793 RNAsubopt: 0.656 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs HotKnots Matthews Correlation Coefficient MXScarna(seed): 0.754 HotKnots: 0.677 Sensitivity MXScarna(seed): 0.718 HotKnots: 0.678 Positive Predictive Value MXScarna(seed): 0.796 HotKnots: 0.680 Number of pairs reference - predicted secondary structure: 229 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNAfold Matthews Correlation Coefficient MXScarna(seed): 0.750 RNAfold: 0.681 Sensitivity MXScarna(seed): 0.712 RNAfold: 0.678 Positive Predictive Value MXScarna(seed): 0.793 RNAfold: 0.688 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNAshapes Matthews Correlation Coefficient MXScarna(seed): 0.750 RNAshapes: 0.669 Sensitivity MXScarna(seed): 0.712 RNAshapes: 0.666 Positive Predictive Value MXScarna(seed): 0.793 RNAshapes: 0.676 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNASampler(seed) Matthews Correlation Coefficient MXScarna(seed): 0.706 RNASampler(seed): 0.557 Sensitivity MXScarna(seed): 0.670 RNASampler(seed): 0.389 Positive Predictive Value MXScarna(seed): 0.748 RNASampler(seed): 0.802 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Afold Matthews Correlation Coefficient MXScarna(seed): 0.744 Afold: 0.641 Sensitivity MXScarna(seed): 0.707 Afold: 0.637 Positive Predictive Value MXScarna(seed): 0.786 Afold: 0.649 Number of pairs reference - predicted secondary structure: 167 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Pknots Matthews Correlation Coefficient MXScarna(seed): 0.748 Pknots: 0.532 Sensitivity MXScarna(seed): 0.715 Pknots: 0.527 Positive Predictive Value MXScarna(seed): 0.787 Pknots: 0.545 Number of pairs reference - predicted secondary structure: 157 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs McQFold Matthews Correlation Coefficient MXScarna(seed): 0.750 McQFold: 0.564 Sensitivity MXScarna(seed): 0.712 McQFold: 0.540 Positive Predictive Value MXScarna(seed): 0.793 McQFold: 0.595 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Carnac(20) Matthews Correlation Coefficient MXScarna(seed): 0.792 Carnac(20): 0.510 Sensitivity MXScarna(seed): 0.756 Carnac(20): 0.302 Positive Predictive Value MXScarna(seed): 0.832 Carnac(20): 0.867 Number of pairs reference - predicted secondary structure: 153 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RNASLOpt Matthews Correlation Coefficient MXScarna(seed): 0.750 RNASLOpt: 0.574 Sensitivity MXScarna(seed): 0.712 RNASLOpt: 0.526 Positive Predictive Value MXScarna(seed): 0.793 RNASLOpt: 0.630 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Cylofold Matthews Correlation Coefficient MXScarna(seed): 0.760 Cylofold: 0.520 Sensitivity MXScarna(seed): 0.725 Cylofold: 0.495 Positive Predictive Value MXScarna(seed): 0.801 Cylofold: 0.552 Number of pairs reference - predicted secondary structure: 214 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Multilign(seed) Matthews Correlation Coefficient MXScarna(seed): 0.557 Multilign(seed): 0.485 Sensitivity MXScarna(seed): 0.540 Multilign(seed): 0.386 Positive Predictive Value MXScarna(seed): 0.583 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.54914456376e-08	+ MXScarna(seed) vs RNAwolf Matthews Correlation Coefficient MXScarna(seed): 0.750 RNAwolf: 0.522 Sensitivity MXScarna(seed): 0.712 RNAwolf: 0.528 Positive Predictive Value MXScarna(seed): 0.793 RNAwolf: 0.522 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs PPfold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.762 PPfold(seed): 0.380 Sensitivity MXScarna(seed): 0.736 PPfold(seed): 0.170 Positive Predictive Value MXScarna(seed): 0.794 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Murlet(seed) Matthews Correlation Coefficient MXScarna(seed): 0.712 Murlet(seed): 0.468 Sensitivity MXScarna(seed): 0.676 Murlet(seed): 0.266 Positive Predictive Value MXScarna(seed): 0.754 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Alterna Matthews Correlation Coefficient MXScarna(seed): 0.749 Alterna: 0.560 Sensitivity MXScarna(seed): 0.715 Alterna: 0.552 Positive Predictive Value MXScarna(seed): 0.788 Alterna: 0.575 Number of pairs reference - predicted secondary structure: 156 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(seed): 0.742 Carnac(seed): 0.415 Sensitivity MXScarna(seed): 0.707 Carnac(seed): 0.196 Positive Predictive Value MXScarna(seed): 0.782 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Vsfold4 Matthews Correlation Coefficient MXScarna(seed): 0.750 Vsfold4: 0.368 Sensitivity MXScarna(seed): 0.712 Vsfold4: 0.337 Positive Predictive Value MXScarna(seed): 0.793 Vsfold4: 0.409 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(seed): 0.739 RSpredict(seed): 0.373 Sensitivity MXScarna(seed): 0.701 RSpredict(seed): 0.251 Positive Predictive Value MXScarna(seed): 0.783 RSpredict(seed): 0.562 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Vsfold5 Matthews Correlation Coefficient MXScarna(seed): 0.750 Vsfold5: 0.328 Sensitivity MXScarna(seed): 0.712 Vsfold5: 0.309 Positive Predictive Value MXScarna(seed): 0.793 Vsfold5: 0.356 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs RDfolder Matthews Correlation Coefficient MXScarna(seed): 0.749 RDfolder: 0.487 Sensitivity MXScarna(seed): 0.715 RDfolder: 0.421 Positive Predictive Value MXScarna(seed): 0.788 RDfolder: 0.571 Number of pairs reference - predicted secondary structure: 156 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs MCFold Matthews Correlation Coefficient MXScarna(seed): 0.752 MCFold: 0.472 Sensitivity MXScarna(seed): 0.715 MCFold: 0.525 Positive Predictive Value MXScarna(seed): 0.793 MCFold: 0.432 Number of pairs reference - predicted secondary structure: 198 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs NanoFolder Matthews Correlation Coefficient MXScarna(seed): 0.774 NanoFolder: 0.372 Sensitivity MXScarna(seed): 0.736 NanoFolder: 0.427 Positive Predictive Value MXScarna(seed): 0.817 NanoFolder: 0.332 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(seed) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(seed): 0.750 Mastr(seed): 0.264 Sensitivity MXScarna(seed): 0.712 Mastr(seed): 0.089 Positive Predictive Value MXScarna(seed): 0.793 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08
CentroidAlifold(20)	320 ContextFold vs CentroidAlifold(20) Matthews Correlation Coefficient ContextFold: 0.923 CentroidAlifold(20): 0.849 Sensitivity ContextFold: 0.898 CentroidAlifold(20): 0.754 Positive Predictive Value ContextFold: 0.949 CentroidAlifold(20): 0.957 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 TurboFold(20) vs CentroidAlifold(20) Matthews Correlation Coefficient TurboFold(20): 0.889 CentroidAlifold(20): 0.849 Sensitivity TurboFold(20): 0.861 CentroidAlifold(20): 0.754 Positive Predictive Value TurboFold(20): 0.919 CentroidAlifold(20): 0.957 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	141 CentroidAlifold(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.815 CentroidAlifold(20): 0.702 Sensitivity CentroidAlifold(seed): 0.743 CentroidAlifold(20): 0.525 Positive Predictive Value CentroidAlifold(seed): 0.897 CentroidAlifold(20): 0.944 Number of pairs reference - predicted secondary structure: 141 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 CentroidHomfold‑LAST vs CentroidAlifold(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.858 CentroidAlifold(20): 0.849 Sensitivity CentroidHomfold‑LAST: 0.821 CentroidAlifold(20): 0.754 Positive Predictive Value CentroidHomfold‑LAST: 0.900 CentroidAlifold(20): 0.957 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	319 PETfold_pre2.0(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.885 CentroidAlifold(20): 0.849 Sensitivity PETfold_pre2.0(seed): 0.832 CentroidAlifold(20): 0.754 Positive Predictive Value PETfold_pre2.0(seed): 0.944 CentroidAlifold(20): 0.958 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 TurboFold(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient TurboFold(seed): 0.880 CentroidAlifold(20): 0.703 Sensitivity TurboFold(seed): 0.875 CentroidAlifold(20): 0.534 Positive Predictive Value TurboFold(seed): 0.886 CentroidAlifold(20): 0.928 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.74172190343e-08	153 MXScarna(seed) vs CentroidAlifold(20) Matthews Correlation Coefficient MXScarna(seed): 0.792 CentroidAlifold(20): 0.725 Sensitivity MXScarna(seed): 0.756 CentroidAlifold(20): 0.558 Positive Predictive Value MXScarna(seed): 0.832 CentroidAlifold(20): 0.946 Number of pairs reference - predicted secondary structure: 153 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ CentroidAlifold(20) vs PETfold_pre2.0(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.849 PETfold_pre2.0(20): 0.847 Sensitivity CentroidAlifold(20): 0.754 PETfold_pre2.0(20): 0.737 Positive Predictive Value CentroidAlifold(20): 0.957 PETfold_pre2.0(20): 0.975 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 2.23046259944e-06	+ CentroidAlifold(20) vs MXScarna(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.849 MXScarna(20): 0.838 Sensitivity CentroidAlifold(20): 0.754 MXScarna(20): 0.791 Positive Predictive Value CentroidAlifold(20): 0.957 MXScarna(20): 0.891 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs PPfold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.854 PPfold(20): 0.839 Sensitivity CentroidAlifold(20): 0.763 PPfold(20): 0.721 Positive Predictive Value CentroidAlifold(20): 0.957 PPfold(20): 0.977 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNAalifold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.849 RNAalifold(20): 0.816 Sensitivity CentroidAlifold(20): 0.754 RNAalifold(20): 0.690 Positive Predictive Value CentroidAlifold(20): 0.957 RNAalifold(20): 0.966 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.849 RSpredict(20): 0.789 Sensitivity CentroidAlifold(20): 0.754 RSpredict(20): 0.693 Positive Predictive Value CentroidAlifold(20): 0.957 RSpredict(20): 0.901 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs IPknot Matthews Correlation Coefficient CentroidAlifold(20): 0.849 IPknot: 0.783 Sensitivity CentroidAlifold(20): 0.754 IPknot: 0.761 Positive Predictive Value CentroidAlifold(20): 0.957 IPknot: 0.807 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.857 Multilign(20): 0.784 Sensitivity CentroidAlifold(20): 0.769 Multilign(20): 0.697 Positive Predictive Value CentroidAlifold(20): 0.957 Multilign(20): 0.885 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(20): 0.849 CentroidFold: 0.735 Sensitivity CentroidAlifold(20): 0.754 CentroidFold: 0.710 Positive Predictive Value CentroidAlifold(20): 0.957 CentroidFold: 0.764 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(20): 0.849 Contrafold: 0.733 Sensitivity CentroidAlifold(20): 0.754 Contrafold: 0.729 Positive Predictive Value CentroidAlifold(20): 0.957 Contrafold: 0.740 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNASampler(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.852 RNASampler(20): 0.770 Sensitivity CentroidAlifold(20): 0.759 RNASampler(20): 0.622 Positive Predictive Value CentroidAlifold(20): 0.957 RNASampler(20): 0.957 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.849 Murlet(20): 0.750 Sensitivity CentroidAlifold(20): 0.754 Murlet(20): 0.619 Positive Predictive Value CentroidAlifold(20): 0.958 Murlet(20): 0.913 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs CMfinder(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.805 CMfinder(seed): 0.736 Sensitivity CentroidAlifold(20): 0.718 CMfinder(seed): 0.607 Positive Predictive Value CentroidAlifold(20): 0.907 CMfinder(seed): 0.898 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ CentroidAlifold(20) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(20): 0.849 MaxExpect: 0.711 Sensitivity CentroidAlifold(20): 0.754 MaxExpect: 0.701 Positive Predictive Value CentroidAlifold(20): 0.957 MaxExpect: 0.725 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs CMfinder(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.854 CMfinder(20): 0.735 Sensitivity CentroidAlifold(20): 0.763 CMfinder(20): 0.603 Positive Predictive Value CentroidAlifold(20): 0.957 CMfinder(20): 0.899 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs CRWrnafold Matthews Correlation Coefficient CentroidAlifold(20): 0.849 CRWrnafold: 0.783 Sensitivity CentroidAlifold(20): 0.754 CRWrnafold: 0.771 Positive Predictive Value CentroidAlifold(20): 0.957 CRWrnafold: 0.798 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(20): 0.849 ProbKnot: 0.707 Sensitivity CentroidAlifold(20): 0.754 ProbKnot: 0.702 Positive Predictive Value CentroidAlifold(20): 0.957 ProbKnot: 0.716 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.849 Mastr(20): 0.708 Sensitivity CentroidAlifold(20): 0.754 Mastr(20): 0.635 Positive Predictive Value CentroidAlifold(20): 0.957 Mastr(20): 0.793 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Fold Matthews Correlation Coefficient CentroidAlifold(20): 0.849 Fold: 0.712 Sensitivity CentroidAlifold(20): 0.754 Fold: 0.710 Positive Predictive Value CentroidAlifold(20): 0.957 Fold: 0.717 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(20): 0.849 UNAFold: 0.708 Sensitivity CentroidAlifold(20): 0.754 UNAFold: 0.696 Positive Predictive Value CentroidAlifold(20): 0.957 UNAFold: 0.723 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(20): 0.849 PknotsRG: 0.691 Sensitivity CentroidAlifold(20): 0.754 PknotsRG: 0.687 Positive Predictive Value CentroidAlifold(20): 0.957 PknotsRG: 0.699 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Sfold Matthews Correlation Coefficient CentroidAlifold(20): 0.849 Sfold: 0.698 Sensitivity CentroidAlifold(20): 0.754 Sfold: 0.662 Positive Predictive Value CentroidAlifold(20): 0.957 Sfold: 0.740 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.694 RNAalifold(seed): 0.604 Sensitivity CentroidAlifold(20): 0.513 RNAalifold(seed): 0.383 Positive Predictive Value CentroidAlifold(20): 0.942 RNAalifold(seed): 0.956 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(20): 0.849 RNAsubopt: 0.694 Sensitivity CentroidAlifold(20): 0.754 RNAsubopt: 0.693 Positive Predictive Value CentroidAlifold(20): 0.957 RNAsubopt: 0.700 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(20): 0.849 HotKnots: 0.698 Sensitivity CentroidAlifold(20): 0.754 HotKnots: 0.695 Positive Predictive Value CentroidAlifold(20): 0.957 HotKnots: 0.705 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(20): 0.849 RNAfold: 0.686 Sensitivity CentroidAlifold(20): 0.754 RNAfold: 0.681 Positive Predictive Value CentroidAlifold(20): 0.957 RNAfold: 0.695 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(20): 0.849 RNAshapes: 0.693 Sensitivity CentroidAlifold(20): 0.754 RNAshapes: 0.687 Positive Predictive Value CentroidAlifold(20): 0.957 RNAshapes: 0.702 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNASampler(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.822 RNASampler(seed): 0.571 Sensitivity CentroidAlifold(20): 0.739 RNASampler(seed): 0.343 Positive Predictive Value CentroidAlifold(20): 0.917 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Afold Matthews Correlation Coefficient CentroidAlifold(20): 0.792 Afold: 0.643 Sensitivity CentroidAlifold(20): 0.668 Afold: 0.632 Positive Predictive Value CentroidAlifold(20): 0.941 Afold: 0.659 Number of pairs reference - predicted secondary structure: 163 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Pknots Matthews Correlation Coefficient CentroidAlifold(20): 0.906 Pknots: 0.655 Sensitivity CentroidAlifold(20): 0.843 Pknots: 0.662 Positive Predictive Value CentroidAlifold(20): 0.974 Pknots: 0.653 Number of pairs reference - predicted secondary structure: 212 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs McQFold Matthews Correlation Coefficient CentroidAlifold(20): 0.849 McQFold: 0.610 Sensitivity CentroidAlifold(20): 0.754 McQFold: 0.587 Positive Predictive Value CentroidAlifold(20): 0.957 McQFold: 0.639 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.849 Carnac(20): 0.675 Sensitivity CentroidAlifold(20): 0.754 Carnac(20): 0.500 Positive Predictive Value CentroidAlifold(20): 0.957 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(20): 0.849 RNASLOpt: 0.638 Sensitivity CentroidAlifold(20): 0.754 RNASLOpt: 0.594 Positive Predictive Value CentroidAlifold(20): 0.957 RNASLOpt: 0.690 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Cylofold Matthews Correlation Coefficient CentroidAlifold(20): 0.849 Cylofold: 0.557 Sensitivity CentroidAlifold(20): 0.753 Cylofold: 0.543 Positive Predictive Value CentroidAlifold(20): 0.959 Cylofold: 0.577 Number of pairs reference - predicted secondary structure: 304 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CentroidAlifold(20) vs Multilign(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.693 Multilign(seed): 0.334 Sensitivity CentroidAlifold(20): 0.581 Multilign(seed): 0.186 Positive Predictive Value CentroidAlifold(20): 0.833 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ CentroidAlifold(20) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(20): 0.849 RNAwolf: 0.561 Sensitivity CentroidAlifold(20): 0.754 RNAwolf: 0.565 Positive Predictive Value CentroidAlifold(20): 0.957 RNAwolf: 0.561 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs PPfold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.702 PPfold(seed): 0.344 Sensitivity CentroidAlifold(20): 0.525 PPfold(seed): 0.128 Positive Predictive Value CentroidAlifold(20): 0.942 PPfold(seed): 0.927 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 4.98172311752e-08	+ CentroidAlifold(20) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.788 Murlet(seed): 0.636 Sensitivity CentroidAlifold(20): 0.679 Murlet(seed): 0.428 Positive Predictive Value CentroidAlifold(20): 0.919 Murlet(seed): 0.952 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Alterna Matthews Correlation Coefficient CentroidAlifold(20): 0.907 Alterna: 0.618 Sensitivity CentroidAlifold(20): 0.844 Alterna: 0.626 Positive Predictive Value CentroidAlifold(20): 0.977 Alterna: 0.616 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.760 Carnac(seed): 0.431 Sensitivity CentroidAlifold(20): 0.625 Carnac(seed): 0.206 Positive Predictive Value CentroidAlifold(20): 0.928 Carnac(seed): 0.907 Number of pairs reference - predicted secondary structure: 68 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(20): 0.849 Vsfold4: 0.502 Sensitivity CentroidAlifold(20): 0.754 Vsfold4: 0.466 Positive Predictive Value CentroidAlifold(20): 0.957 Vsfold4: 0.546 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.702 RSpredict(seed): 0.414 Sensitivity CentroidAlifold(20): 0.525 RSpredict(seed): 0.279 Positive Predictive Value CentroidAlifold(20): 0.944 RSpredict(seed): 0.622 Number of pairs reference - predicted secondary structure: 141 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(20): 0.849 Vsfold5: 0.457 Sensitivity CentroidAlifold(20): 0.754 Vsfold5: 0.437 Positive Predictive Value CentroidAlifold(20): 0.957 Vsfold5: 0.484 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(20): 0.907 RDfolder: 0.556 Sensitivity CentroidAlifold(20): 0.844 RDfolder: 0.511 Positive Predictive Value CentroidAlifold(20): 0.977 RDfolder: 0.611 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs MCFold Matthews Correlation Coefficient CentroidAlifold(20): 0.840 MCFold: 0.500 Sensitivity CentroidAlifold(20): 0.742 MCFold: 0.559 Positive Predictive Value CentroidAlifold(20): 0.953 MCFold: 0.453 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(20): 0.794 NanoFolder: 0.337 Sensitivity CentroidAlifold(20): 0.666 NanoFolder: 0.391 Positive Predictive Value CentroidAlifold(20): 0.949 NanoFolder: 0.298 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidAlifold(20) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.727 Mastr(seed): 0.265 Sensitivity CentroidAlifold(20): 0.560 Mastr(seed): 0.087 Positive Predictive Value CentroidAlifold(20): 0.946 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 154 Wilcoxon single-rank test P-value: 3.56938820447e-08
PETfold_pre2.0(20)	320 ContextFold vs PETfold_pre2.0(20) Matthews Correlation Coefficient ContextFold: 0.923 PETfold_pre2.0(20): 0.847 Sensitivity ContextFold: 0.898 PETfold_pre2.0(20): 0.737 Positive Predictive Value ContextFold: 0.949 PETfold_pre2.0(20): 0.975 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 TurboFold(20) vs PETfold_pre2.0(20) Matthews Correlation Coefficient TurboFold(20): 0.889 PETfold_pre2.0(20): 0.847 Sensitivity TurboFold(20): 0.861 PETfold_pre2.0(20): 0.737 Positive Predictive Value TurboFold(20): 0.919 PETfold_pre2.0(20): 0.975 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	141 CentroidAlifold(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.815 PETfold_pre2.0(20): 0.641 Sensitivity CentroidAlifold(seed): 0.743 PETfold_pre2.0(20): 0.440 Positive Predictive Value CentroidAlifold(seed): 0.897 PETfold_pre2.0(20): 0.938 Number of pairs reference - predicted secondary structure: 141 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 CentroidHomfold‑LAST vs PETfold_pre2.0(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.858 PETfold_pre2.0(20): 0.847 Sensitivity CentroidHomfold‑LAST: 0.821 PETfold_pre2.0(20): 0.737 Positive Predictive Value CentroidHomfold‑LAST: 0.900 PETfold_pre2.0(20): 0.975 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	319 PETfold_pre2.0(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.885 PETfold_pre2.0(20): 0.848 Sensitivity PETfold_pre2.0(seed): 0.832 PETfold_pre2.0(20): 0.739 Positive Predictive Value PETfold_pre2.0(seed): 0.944 PETfold_pre2.0(20): 0.976 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 TurboFold(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient TurboFold(seed): 0.880 PETfold_pre2.0(20): 0.648 Sensitivity TurboFold(seed): 0.875 PETfold_pre2.0(20): 0.451 Positive Predictive Value TurboFold(seed): 0.886 PETfold_pre2.0(20): 0.934 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.62913390836e-08	153 MXScarna(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient MXScarna(seed): 0.792 PETfold_pre2.0(20): 0.674 Sensitivity MXScarna(seed): 0.756 PETfold_pre2.0(20): 0.483 Positive Predictive Value MXScarna(seed): 0.832 PETfold_pre2.0(20): 0.943 Number of pairs reference - predicted secondary structure: 153 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 CentroidAlifold(20) vs PETfold_pre2.0(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.849 PETfold_pre2.0(20): 0.847 Sensitivity CentroidAlifold(20): 0.754 PETfold_pre2.0(20): 0.737 Positive Predictive Value CentroidAlifold(20): 0.957 PETfold_pre2.0(20): 0.975 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 2.23046259944e-06		+ PETfold_pre2.0(20) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 MXScarna(20): 0.838 Sensitivity PETfold_pre2.0(20): 0.737 MXScarna(20): 0.791 Positive Predictive Value PETfold_pre2.0(20): 0.975 MXScarna(20): 0.891 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs PPfold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.853 PPfold(20): 0.839 Sensitivity PETfold_pre2.0(20): 0.748 PPfold(20): 0.721 Positive Predictive Value PETfold_pre2.0(20): 0.975 PPfold(20): 0.977 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 RNAalifold(20): 0.816 Sensitivity PETfold_pre2.0(20): 0.737 RNAalifold(20): 0.690 Positive Predictive Value PETfold_pre2.0(20): 0.975 RNAalifold(20): 0.966 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 RSpredict(20): 0.789 Sensitivity PETfold_pre2.0(20): 0.737 RSpredict(20): 0.693 Positive Predictive Value PETfold_pre2.0(20): 0.975 RSpredict(20): 0.901 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 IPknot: 0.783 Sensitivity PETfold_pre2.0(20): 0.737 IPknot: 0.761 Positive Predictive Value PETfold_pre2.0(20): 0.975 IPknot: 0.807 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.858 Multilign(20): 0.784 Sensitivity PETfold_pre2.0(20): 0.756 Multilign(20): 0.697 Positive Predictive Value PETfold_pre2.0(20): 0.975 Multilign(20): 0.885 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 CentroidFold: 0.735 Sensitivity PETfold_pre2.0(20): 0.737 CentroidFold: 0.710 Positive Predictive Value PETfold_pre2.0(20): 0.975 CentroidFold: 0.764 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 Contrafold: 0.733 Sensitivity PETfold_pre2.0(20): 0.737 Contrafold: 0.729 Positive Predictive Value PETfold_pre2.0(20): 0.975 Contrafold: 0.740 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.850 RNASampler(20): 0.770 Sensitivity PETfold_pre2.0(20): 0.743 RNASampler(20): 0.622 Positive Predictive Value PETfold_pre2.0(20): 0.975 RNASampler(20): 0.957 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.848 Murlet(20): 0.750 Sensitivity PETfold_pre2.0(20): 0.739 Murlet(20): 0.619 Positive Predictive Value PETfold_pre2.0(20): 0.976 Murlet(20): 0.913 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CMfinder(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient CMfinder(seed): 0.736 PETfold_pre2.0(20): 0.708 Sensitivity CMfinder(seed): 0.607 PETfold_pre2.0(20): 0.594 Positive Predictive Value CMfinder(seed): 0.898 PETfold_pre2.0(20): 0.851 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ PETfold_pre2.0(20) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 MaxExpect: 0.711 Sensitivity PETfold_pre2.0(20): 0.737 MaxExpect: 0.701 Positive Predictive Value PETfold_pre2.0(20): 0.975 MaxExpect: 0.725 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.852 CMfinder(20): 0.735 Sensitivity PETfold_pre2.0(20): 0.746 CMfinder(20): 0.603 Positive Predictive Value PETfold_pre2.0(20): 0.975 CMfinder(20): 0.899 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs CRWrnafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 CRWrnafold: 0.783 Sensitivity PETfold_pre2.0(20): 0.737 CRWrnafold: 0.771 Positive Predictive Value PETfold_pre2.0(20): 0.975 CRWrnafold: 0.798 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 ProbKnot: 0.707 Sensitivity PETfold_pre2.0(20): 0.737 ProbKnot: 0.702 Positive Predictive Value PETfold_pre2.0(20): 0.975 ProbKnot: 0.716 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 Mastr(20): 0.708 Sensitivity PETfold_pre2.0(20): 0.737 Mastr(20): 0.635 Positive Predictive Value PETfold_pre2.0(20): 0.975 Mastr(20): 0.793 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 Fold: 0.712 Sensitivity PETfold_pre2.0(20): 0.737 Fold: 0.710 Positive Predictive Value PETfold_pre2.0(20): 0.975 Fold: 0.717 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 UNAFold: 0.708 Sensitivity PETfold_pre2.0(20): 0.737 UNAFold: 0.696 Positive Predictive Value PETfold_pre2.0(20): 0.975 UNAFold: 0.723 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 PknotsRG: 0.691 Sensitivity PETfold_pre2.0(20): 0.737 PknotsRG: 0.687 Positive Predictive Value PETfold_pre2.0(20): 0.975 PknotsRG: 0.699 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 Sfold: 0.698 Sensitivity PETfold_pre2.0(20): 0.737 Sfold: 0.662 Positive Predictive Value PETfold_pre2.0(20): 0.975 Sfold: 0.740 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RNAalifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.630 RNAalifold(seed): 0.604 Sensitivity PETfold_pre2.0(20): 0.426 RNAalifold(seed): 0.383 Positive Predictive Value PETfold_pre2.0(20): 0.935 RNAalifold(seed): 0.956 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 RNAsubopt: 0.694 Sensitivity PETfold_pre2.0(20): 0.737 RNAsubopt: 0.693 Positive Predictive Value PETfold_pre2.0(20): 0.975 RNAsubopt: 0.700 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs HotKnots Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 HotKnots: 0.698 Sensitivity PETfold_pre2.0(20): 0.737 HotKnots: 0.695 Positive Predictive Value PETfold_pre2.0(20): 0.975 HotKnots: 0.705 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 RNAfold: 0.686 Sensitivity PETfold_pre2.0(20): 0.737 RNAfold: 0.681 Positive Predictive Value PETfold_pre2.0(20): 0.975 RNAfold: 0.695 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 RNAshapes: 0.693 Sensitivity PETfold_pre2.0(20): 0.737 RNAshapes: 0.687 Positive Predictive Value PETfold_pre2.0(20): 0.975 RNAshapes: 0.702 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RNASampler(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 RNASampler(seed): 0.571 Sensitivity PETfold_pre2.0(20): 0.627 RNASampler(seed): 0.343 Positive Predictive Value PETfold_pre2.0(20): 0.867 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.777 Afold: 0.643 Sensitivity PETfold_pre2.0(20): 0.632 Afold: 0.632 Positive Predictive Value PETfold_pre2.0(20): 0.957 Afold: 0.659 Number of pairs reference - predicted secondary structure: 163 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Pknots Matthews Correlation Coefficient PETfold_pre2.0(20): 0.885 Pknots: 0.655 Sensitivity PETfold_pre2.0(20): 0.807 Pknots: 0.662 Positive Predictive Value PETfold_pre2.0(20): 0.972 Pknots: 0.653 Number of pairs reference - predicted secondary structure: 212 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 McQFold: 0.610 Sensitivity PETfold_pre2.0(20): 0.737 McQFold: 0.587 Positive Predictive Value PETfold_pre2.0(20): 0.975 McQFold: 0.639 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 Carnac(20): 0.675 Sensitivity PETfold_pre2.0(20): 0.737 Carnac(20): 0.500 Positive Predictive Value PETfold_pre2.0(20): 0.975 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 RNASLOpt: 0.638 Sensitivity PETfold_pre2.0(20): 0.737 RNASLOpt: 0.594 Positive Predictive Value PETfold_pre2.0(20): 0.975 RNASLOpt: 0.690 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Cylofold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.845 Cylofold: 0.557 Sensitivity PETfold_pre2.0(20): 0.735 Cylofold: 0.543 Positive Predictive Value PETfold_pre2.0(20): 0.974 Cylofold: 0.577 Number of pairs reference - predicted secondary structure: 304 Wilcoxon single-rank test P-value: 3.56938820447e-08	? PETfold_pre2.0(20) vs Multilign(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.473 Multilign(seed): 0.334 Sensitivity PETfold_pre2.0(20): 0.326 Multilign(seed): 0.186 Positive Predictive Value PETfold_pre2.0(20): 0.700 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ PETfold_pre2.0(20) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 RNAwolf: 0.561 Sensitivity PETfold_pre2.0(20): 0.737 RNAwolf: 0.565 Positive Predictive Value PETfold_pre2.0(20): 0.975 RNAwolf: 0.561 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs PPfold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.616 PPfold(seed): 0.344 Sensitivity PETfold_pre2.0(20): 0.400 PPfold(seed): 0.128 Positive Predictive Value PETfold_pre2.0(20): 0.952 PPfold(seed): 0.927 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ PETfold_pre2.0(20) vs Murlet(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.707 Murlet(seed): 0.636 Sensitivity PETfold_pre2.0(20): 0.578 Murlet(seed): 0.428 Positive Predictive Value PETfold_pre2.0(20): 0.871 Murlet(seed): 0.952 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Alterna Matthews Correlation Coefficient PETfold_pre2.0(20): 0.887 Alterna: 0.618 Sensitivity PETfold_pre2.0(20): 0.811 Alterna: 0.626 Positive Predictive Value PETfold_pre2.0(20): 0.973 Alterna: 0.616 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.692 Carnac(seed): 0.431 Sensitivity PETfold_pre2.0(20): 0.533 Carnac(seed): 0.206 Positive Predictive Value PETfold_pre2.0(20): 0.904 Carnac(seed): 0.907 Number of pairs reference - predicted secondary structure: 68 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 Vsfold4: 0.502 Sensitivity PETfold_pre2.0(20): 0.737 Vsfold4: 0.466 Positive Predictive Value PETfold_pre2.0(20): 0.975 Vsfold4: 0.546 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.641 RSpredict(seed): 0.414 Sensitivity PETfold_pre2.0(20): 0.440 RSpredict(seed): 0.279 Positive Predictive Value PETfold_pre2.0(20): 0.938 RSpredict(seed): 0.622 Number of pairs reference - predicted secondary structure: 141 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 Vsfold5: 0.457 Sensitivity PETfold_pre2.0(20): 0.737 Vsfold5: 0.437 Positive Predictive Value PETfold_pre2.0(20): 0.975 Vsfold5: 0.484 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs RDfolder Matthews Correlation Coefficient PETfold_pre2.0(20): 0.887 RDfolder: 0.556 Sensitivity PETfold_pre2.0(20): 0.811 RDfolder: 0.511 Positive Predictive Value PETfold_pre2.0(20): 0.973 RDfolder: 0.611 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.838 MCFold: 0.500 Sensitivity PETfold_pre2.0(20): 0.724 MCFold: 0.559 Positive Predictive Value PETfold_pre2.0(20): 0.973 MCFold: 0.453 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(20): 0.794 NanoFolder: 0.337 Sensitivity PETfold_pre2.0(20): 0.654 NanoFolder: 0.391 Positive Predictive Value PETfold_pre2.0(20): 0.967 NanoFolder: 0.298 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PETfold_pre2.0(20) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.676 Mastr(seed): 0.265 Sensitivity PETfold_pre2.0(20): 0.486 Mastr(seed): 0.087 Positive Predictive Value PETfold_pre2.0(20): 0.943 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 154 Wilcoxon single-rank test P-value: 3.56938820447e-08
MXScarna(20)	320 ContextFold vs MXScarna(20) Matthews Correlation Coefficient ContextFold: 0.923 MXScarna(20): 0.838 Sensitivity ContextFold: 0.898 MXScarna(20): 0.791 Positive Predictive Value ContextFold: 0.949 MXScarna(20): 0.891 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 TurboFold(20) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(20): 0.889 MXScarna(20): 0.838 Sensitivity TurboFold(20): 0.861 MXScarna(20): 0.791 Positive Predictive Value TurboFold(20): 0.919 MXScarna(20): 0.891 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	141 CentroidAlifold(seed) vs MXScarna(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.815 MXScarna(20): 0.764 Sensitivity CentroidAlifold(seed): 0.743 MXScarna(20): 0.686 Positive Predictive Value CentroidAlifold(seed): 0.897 MXScarna(20): 0.854 Number of pairs reference - predicted secondary structure: 141 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 CentroidHomfold‑LAST vs MXScarna(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.858 MXScarna(20): 0.838 Sensitivity CentroidHomfold‑LAST: 0.821 MXScarna(20): 0.791 Positive Predictive Value CentroidHomfold‑LAST: 0.900 MXScarna(20): 0.891 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	319 PETfold_pre2.0(seed) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.885 MXScarna(20): 0.839 Sensitivity PETfold_pre2.0(seed): 0.832 MXScarna(20): 0.791 Positive Predictive Value PETfold_pre2.0(seed): 0.944 MXScarna(20): 0.892 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 TurboFold(seed) vs MXScarna(20) Matthews Correlation Coefficient TurboFold(seed): 0.880 MXScarna(20): 0.864 Sensitivity TurboFold(seed): 0.875 MXScarna(20): 0.836 Positive Predictive Value TurboFold(seed): 0.886 MXScarna(20): 0.895 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.32883086441e-08	153 MXScarna(seed) vs MXScarna(20) Matthews Correlation Coefficient MXScarna(seed): 0.792 MXScarna(20): 0.778 Sensitivity MXScarna(seed): 0.756 MXScarna(20): 0.705 Positive Predictive Value MXScarna(seed): 0.832 MXScarna(20): 0.863 Number of pairs reference - predicted secondary structure: 153 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 CentroidAlifold(20) vs MXScarna(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.849 MXScarna(20): 0.838 Sensitivity CentroidAlifold(20): 0.754 MXScarna(20): 0.791 Positive Predictive Value CentroidAlifold(20): 0.957 MXScarna(20): 0.891 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 PETfold_pre2.0(20) vs MXScarna(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 MXScarna(20): 0.838 Sensitivity PETfold_pre2.0(20): 0.737 MXScarna(20): 0.791 Positive Predictive Value PETfold_pre2.0(20): 0.975 MXScarna(20): 0.891 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ MXScarna(20) vs PPfold(20) Matthews Correlation Coefficient MXScarna(20): 0.842 PPfold(20): 0.839 Sensitivity MXScarna(20): 0.799 PPfold(20): 0.721 Positive Predictive Value MXScarna(20): 0.890 PPfold(20): 0.977 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 2.16217446969e-05	+ MXScarna(20) vs RNAalifold(20) Matthews Correlation Coefficient MXScarna(20): 0.838 RNAalifold(20): 0.816 Sensitivity MXScarna(20): 0.791 RNAalifold(20): 0.690 Positive Predictive Value MXScarna(20): 0.891 RNAalifold(20): 0.966 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(20): 0.838 RSpredict(20): 0.789 Sensitivity MXScarna(20): 0.791 RSpredict(20): 0.693 Positive Predictive Value MXScarna(20): 0.891 RSpredict(20): 0.901 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs IPknot Matthews Correlation Coefficient MXScarna(20): 0.838 IPknot: 0.783 Sensitivity MXScarna(20): 0.791 IPknot: 0.761 Positive Predictive Value MXScarna(20): 0.891 IPknot: 0.807 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Multilign(20) Matthews Correlation Coefficient MXScarna(20): 0.841 Multilign(20): 0.784 Sensitivity MXScarna(20): 0.796 Multilign(20): 0.697 Positive Predictive Value MXScarna(20): 0.890 Multilign(20): 0.885 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs CentroidFold Matthews Correlation Coefficient MXScarna(20): 0.838 CentroidFold: 0.735 Sensitivity MXScarna(20): 0.791 CentroidFold: 0.710 Positive Predictive Value MXScarna(20): 0.891 CentroidFold: 0.764 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Contrafold Matthews Correlation Coefficient MXScarna(20): 0.838 Contrafold: 0.733 Sensitivity MXScarna(20): 0.791 Contrafold: 0.729 Positive Predictive Value MXScarna(20): 0.891 Contrafold: 0.740 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RNASampler(20) Matthews Correlation Coefficient MXScarna(20): 0.841 RNASampler(20): 0.770 Sensitivity MXScarna(20): 0.796 RNASampler(20): 0.622 Positive Predictive Value MXScarna(20): 0.890 RNASampler(20): 0.957 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Murlet(20) Matthews Correlation Coefficient MXScarna(20): 0.839 Murlet(20): 0.750 Sensitivity MXScarna(20): 0.791 Murlet(20): 0.619 Positive Predictive Value MXScarna(20): 0.892 Murlet(20): 0.913 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs CMfinder(seed) Matthews Correlation Coefficient MXScarna(20): 0.820 CMfinder(seed): 0.736 Sensitivity MXScarna(20): 0.785 CMfinder(seed): 0.607 Positive Predictive Value MXScarna(20): 0.860 CMfinder(seed): 0.898 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs MaxExpect Matthews Correlation Coefficient MXScarna(20): 0.838 MaxExpect: 0.711 Sensitivity MXScarna(20): 0.791 MaxExpect: 0.701 Positive Predictive Value MXScarna(20): 0.891 MaxExpect: 0.725 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(20): 0.843 CMfinder(20): 0.735 Sensitivity MXScarna(20): 0.800 CMfinder(20): 0.603 Positive Predictive Value MXScarna(20): 0.890 CMfinder(20): 0.899 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs CRWrnafold Matthews Correlation Coefficient MXScarna(20): 0.838 CRWrnafold: 0.783 Sensitivity MXScarna(20): 0.791 CRWrnafold: 0.771 Positive Predictive Value MXScarna(20): 0.891 CRWrnafold: 0.798 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs ProbKnot Matthews Correlation Coefficient MXScarna(20): 0.838 ProbKnot: 0.707 Sensitivity MXScarna(20): 0.791 ProbKnot: 0.702 Positive Predictive Value MXScarna(20): 0.891 ProbKnot: 0.716 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Mastr(20) Matthews Correlation Coefficient MXScarna(20): 0.838 Mastr(20): 0.708 Sensitivity MXScarna(20): 0.791 Mastr(20): 0.635 Positive Predictive Value MXScarna(20): 0.891 Mastr(20): 0.793 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Fold Matthews Correlation Coefficient MXScarna(20): 0.838 Fold: 0.712 Sensitivity MXScarna(20): 0.791 Fold: 0.710 Positive Predictive Value MXScarna(20): 0.891 Fold: 0.717 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs UNAFold Matthews Correlation Coefficient MXScarna(20): 0.838 UNAFold: 0.708 Sensitivity MXScarna(20): 0.791 UNAFold: 0.696 Positive Predictive Value MXScarna(20): 0.891 UNAFold: 0.723 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs PknotsRG Matthews Correlation Coefficient MXScarna(20): 0.838 PknotsRG: 0.691 Sensitivity MXScarna(20): 0.791 PknotsRG: 0.687 Positive Predictive Value MXScarna(20): 0.891 PknotsRG: 0.699 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Sfold Matthews Correlation Coefficient MXScarna(20): 0.838 Sfold: 0.698 Sensitivity MXScarna(20): 0.791 Sfold: 0.662 Positive Predictive Value MXScarna(20): 0.891 Sfold: 0.740 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RNAalifold(seed) Matthews Correlation Coefficient MXScarna(20): 0.761 RNAalifold(seed): 0.604 Sensitivity MXScarna(20): 0.682 RNAalifold(seed): 0.383 Positive Predictive Value MXScarna(20): 0.852 RNAalifold(seed): 0.956 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RNAsubopt Matthews Correlation Coefficient MXScarna(20): 0.838 RNAsubopt: 0.694 Sensitivity MXScarna(20): 0.791 RNAsubopt: 0.693 Positive Predictive Value MXScarna(20): 0.891 RNAsubopt: 0.700 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs HotKnots Matthews Correlation Coefficient MXScarna(20): 0.838 HotKnots: 0.698 Sensitivity MXScarna(20): 0.791 HotKnots: 0.695 Positive Predictive Value MXScarna(20): 0.891 HotKnots: 0.705 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RNAfold Matthews Correlation Coefficient MXScarna(20): 0.838 RNAfold: 0.686 Sensitivity MXScarna(20): 0.791 RNAfold: 0.681 Positive Predictive Value MXScarna(20): 0.891 RNAfold: 0.695 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RNAshapes Matthews Correlation Coefficient MXScarna(20): 0.838 RNAshapes: 0.693 Sensitivity MXScarna(20): 0.791 RNAshapes: 0.687 Positive Predictive Value MXScarna(20): 0.891 RNAshapes: 0.702 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RNASampler(seed) Matthews Correlation Coefficient MXScarna(20): 0.835 RNASampler(seed): 0.571 Sensitivity MXScarna(20): 0.800 RNASampler(seed): 0.343 Positive Predictive Value MXScarna(20): 0.874 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Afold Matthews Correlation Coefficient MXScarna(20): 0.805 Afold: 0.643 Sensitivity MXScarna(20): 0.751 Afold: 0.632 Positive Predictive Value MXScarna(20): 0.865 Afold: 0.659 Number of pairs reference - predicted secondary structure: 163 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Pknots Matthews Correlation Coefficient MXScarna(20): 0.872 Pknots: 0.655 Sensitivity MXScarna(20): 0.834 Pknots: 0.662 Positive Predictive Value MXScarna(20): 0.913 Pknots: 0.653 Number of pairs reference - predicted secondary structure: 212 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs McQFold Matthews Correlation Coefficient MXScarna(20): 0.838 McQFold: 0.610 Sensitivity MXScarna(20): 0.791 McQFold: 0.587 Positive Predictive Value MXScarna(20): 0.891 McQFold: 0.639 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Carnac(20) Matthews Correlation Coefficient MXScarna(20): 0.838 Carnac(20): 0.675 Sensitivity MXScarna(20): 0.791 Carnac(20): 0.500 Positive Predictive Value MXScarna(20): 0.891 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RNASLOpt Matthews Correlation Coefficient MXScarna(20): 0.838 RNASLOpt: 0.638 Sensitivity MXScarna(20): 0.791 RNASLOpt: 0.594 Positive Predictive Value MXScarna(20): 0.891 RNASLOpt: 0.690 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Cylofold Matthews Correlation Coefficient MXScarna(20): 0.841 Cylofold: 0.557 Sensitivity MXScarna(20): 0.795 Cylofold: 0.543 Positive Predictive Value MXScarna(20): 0.892 Cylofold: 0.577 Number of pairs reference - predicted secondary structure: 304 Wilcoxon single-rank test P-value: 3.56938820447e-08	? MXScarna(20) vs Multilign(seed) Matthews Correlation Coefficient MXScarna(20): 0.749 Multilign(seed): 0.334 Sensitivity MXScarna(20): 0.698 Multilign(seed): 0.186 Positive Predictive Value MXScarna(20): 0.811 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ MXScarna(20) vs RNAwolf Matthews Correlation Coefficient MXScarna(20): 0.838 RNAwolf: 0.561 Sensitivity MXScarna(20): 0.791 RNAwolf: 0.565 Positive Predictive Value MXScarna(20): 0.891 RNAwolf: 0.561 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs PPfold(seed) Matthews Correlation Coefficient MXScarna(20): 0.831 PPfold(seed): 0.344 Sensitivity MXScarna(20): 0.764 PPfold(seed): 0.128 Positive Predictive Value MXScarna(20): 0.906 PPfold(seed): 0.927 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ MXScarna(20) vs Murlet(seed) Matthews Correlation Coefficient MXScarna(20): 0.834 Murlet(seed): 0.636 Sensitivity MXScarna(20): 0.795 Murlet(seed): 0.428 Positive Predictive Value MXScarna(20): 0.877 Murlet(seed): 0.952 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Alterna Matthews Correlation Coefficient MXScarna(20): 0.873 Alterna: 0.618 Sensitivity MXScarna(20): 0.835 Alterna: 0.626 Positive Predictive Value MXScarna(20): 0.915 Alterna: 0.616 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(20): 0.835 Carnac(seed): 0.431 Sensitivity MXScarna(20): 0.786 Carnac(seed): 0.206 Positive Predictive Value MXScarna(20): 0.890 Carnac(seed): 0.907 Number of pairs reference - predicted secondary structure: 68 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Vsfold4 Matthews Correlation Coefficient MXScarna(20): 0.838 Vsfold4: 0.502 Sensitivity MXScarna(20): 0.791 Vsfold4: 0.466 Positive Predictive Value MXScarna(20): 0.891 Vsfold4: 0.546 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(20): 0.764 RSpredict(seed): 0.414 Sensitivity MXScarna(20): 0.686 RSpredict(seed): 0.279 Positive Predictive Value MXScarna(20): 0.854 RSpredict(seed): 0.622 Number of pairs reference - predicted secondary structure: 141 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Vsfold5 Matthews Correlation Coefficient MXScarna(20): 0.838 Vsfold5: 0.457 Sensitivity MXScarna(20): 0.791 Vsfold5: 0.437 Positive Predictive Value MXScarna(20): 0.891 Vsfold5: 0.484 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs RDfolder Matthews Correlation Coefficient MXScarna(20): 0.873 RDfolder: 0.556 Sensitivity MXScarna(20): 0.835 RDfolder: 0.511 Positive Predictive Value MXScarna(20): 0.915 RDfolder: 0.611 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs MCFold Matthews Correlation Coefficient MXScarna(20): 0.833 MCFold: 0.500 Sensitivity MXScarna(20): 0.786 MCFold: 0.559 Positive Predictive Value MXScarna(20): 0.886 MCFold: 0.453 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs NanoFolder Matthews Correlation Coefficient MXScarna(20): 0.812 NanoFolder: 0.337 Sensitivity MXScarna(20): 0.757 NanoFolder: 0.391 Positive Predictive Value MXScarna(20): 0.875 NanoFolder: 0.298 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MXScarna(20) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(20): 0.779 Mastr(seed): 0.265 Sensitivity MXScarna(20): 0.705 Mastr(seed): 0.087 Positive Predictive Value MXScarna(20): 0.864 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 154 Wilcoxon single-rank test P-value: 3.56938820447e-08
PPfold(20)	314 ContextFold vs PPfold(20) Matthews Correlation Coefficient ContextFold: 0.923 PPfold(20): 0.839 Sensitivity ContextFold: 0.898 PPfold(20): 0.721 Positive Predictive Value ContextFold: 0.951 PPfold(20): 0.977 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	314 TurboFold(20) vs PPfold(20) Matthews Correlation Coefficient TurboFold(20): 0.890 PPfold(20): 0.839 Sensitivity TurboFold(20): 0.862 PPfold(20): 0.721 Positive Predictive Value TurboFold(20): 0.921 PPfold(20): 0.977 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	135 CentroidAlifold(seed) vs PPfold(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.816 PPfold(20): 0.625 Sensitivity CentroidAlifold(seed): 0.741 PPfold(20): 0.415 Positive Predictive Value CentroidAlifold(seed): 0.900 PPfold(20): 0.944 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	314 CentroidHomfold‑LAST vs PPfold(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.859 PPfold(20): 0.839 Sensitivity CentroidHomfold‑LAST: 0.821 PPfold(20): 0.721 Positive Predictive Value CentroidHomfold‑LAST: 0.902 PPfold(20): 0.977 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	313 PETfold_pre2.0(seed) vs PPfold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.889 PPfold(20): 0.840 Sensitivity PETfold_pre2.0(seed): 0.837 PPfold(20): 0.723 Positive Predictive Value PETfold_pre2.0(seed): 0.946 PPfold(20): 0.977 Number of pairs reference - predicted secondary structure: 313 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 TurboFold(seed) vs PPfold(20) Matthews Correlation Coefficient TurboFold(seed): 0.880 PPfold(20): 0.629 Sensitivity TurboFold(seed): 0.875 PPfold(20): 0.417 Positive Predictive Value TurboFold(seed): 0.886 PPfold(20): 0.955 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.97012568641e-08	147 MXScarna(seed) vs PPfold(20) Matthews Correlation Coefficient MXScarna(seed): 0.795 PPfold(20): 0.659 Sensitivity MXScarna(seed): 0.758 PPfold(20): 0.461 Positive Predictive Value MXScarna(seed): 0.837 PPfold(20): 0.948 Number of pairs reference - predicted secondary structure: 147 Wilcoxon single-rank test P-value: 3.56938820447e-08	314 CentroidAlifold(20) vs PPfold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.854 PPfold(20): 0.839 Sensitivity CentroidAlifold(20): 0.763 PPfold(20): 0.721 Positive Predictive Value CentroidAlifold(20): 0.957 PPfold(20): 0.977 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	314 PETfold_pre2.0(20) vs PPfold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.853 PPfold(20): 0.839 Sensitivity PETfold_pre2.0(20): 0.748 PPfold(20): 0.721 Positive Predictive Value PETfold_pre2.0(20): 0.975 PPfold(20): 0.977 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	314 MXScarna(20) vs PPfold(20) Matthews Correlation Coefficient MXScarna(20): 0.842 PPfold(20): 0.839 Sensitivity MXScarna(20): 0.799 PPfold(20): 0.721 Positive Predictive Value MXScarna(20): 0.890 PPfold(20): 0.977 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 2.16217446969e-05		+ PPfold(20) vs RNAalifold(20) Matthews Correlation Coefficient PPfold(20): 0.839 RNAalifold(20): 0.820 Sensitivity PPfold(20): 0.721 RNAalifold(20): 0.698 Positive Predictive Value PPfold(20): 0.977 RNAalifold(20): 0.966 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RSpredict(20) Matthews Correlation Coefficient PPfold(20): 0.839 RSpredict(20): 0.796 Sensitivity PPfold(20): 0.721 RSpredict(20): 0.704 Positive Predictive Value PPfold(20): 0.977 RSpredict(20): 0.902 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs IPknot Matthews Correlation Coefficient PPfold(20): 0.839 IPknot: 0.782 Sensitivity PPfold(20): 0.721 IPknot: 0.760 Positive Predictive Value PPfold(20): 0.977 IPknot: 0.807 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Multilign(20) Matthews Correlation Coefficient PPfold(20): 0.850 Multilign(20): 0.789 Sensitivity PPfold(20): 0.741 Multilign(20): 0.704 Positive Predictive Value PPfold(20): 0.977 Multilign(20): 0.887 Number of pairs reference - predicted secondary structure: 305 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs CentroidFold Matthews Correlation Coefficient PPfold(20): 0.839 CentroidFold: 0.733 Sensitivity PPfold(20): 0.721 CentroidFold: 0.707 Positive Predictive Value PPfold(20): 0.977 CentroidFold: 0.763 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Contrafold Matthews Correlation Coefficient PPfold(20): 0.839 Contrafold: 0.730 Sensitivity PPfold(20): 0.721 Contrafold: 0.726 Positive Predictive Value PPfold(20): 0.977 Contrafold: 0.738 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RNASampler(20) Matthews Correlation Coefficient PPfold(20): 0.841 RNASampler(20): 0.774 Sensitivity PPfold(20): 0.725 RNASampler(20): 0.629 Positive Predictive Value PPfold(20): 0.977 RNASampler(20): 0.956 Number of pairs reference - predicted secondary structure: 310 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Murlet(20) Matthews Correlation Coefficient PPfold(20): 0.840 Murlet(20): 0.754 Sensitivity PPfold(20): 0.723 Murlet(20): 0.625 Positive Predictive Value PPfold(20): 0.977 Murlet(20): 0.912 Number of pairs reference - predicted secondary structure: 313 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CMfinder(seed) vs PPfold(20) Matthews Correlation Coefficient CMfinder(seed): 0.736 PPfold(20): 0.656 Sensitivity CMfinder(seed): 0.607 PPfold(20): 0.507 Positive Predictive Value CMfinder(seed): 0.898 PPfold(20): 0.856 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ PPfold(20) vs MaxExpect Matthews Correlation Coefficient PPfold(20): 0.839 MaxExpect: 0.709 Sensitivity PPfold(20): 0.721 MaxExpect: 0.698 Positive Predictive Value PPfold(20): 0.977 MaxExpect: 0.723 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs CMfinder(20) Matthews Correlation Coefficient PPfold(20): 0.843 CMfinder(20): 0.737 Sensitivity PPfold(20): 0.729 CMfinder(20): 0.607 Positive Predictive Value PPfold(20): 0.977 CMfinder(20): 0.898 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs CRWrnafold Matthews Correlation Coefficient PPfold(20): 0.839 CRWrnafold: 0.782 Sensitivity PPfold(20): 0.721 CRWrnafold: 0.769 Positive Predictive Value PPfold(20): 0.977 CRWrnafold: 0.797 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs ProbKnot Matthews Correlation Coefficient PPfold(20): 0.839 ProbKnot: 0.704 Sensitivity PPfold(20): 0.721 ProbKnot: 0.699 Positive Predictive Value PPfold(20): 0.977 ProbKnot: 0.713 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Mastr(20) Matthews Correlation Coefficient PPfold(20): 0.839 Mastr(20): 0.714 Sensitivity PPfold(20): 0.721 Mastr(20): 0.644 Positive Predictive Value PPfold(20): 0.977 Mastr(20): 0.796 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Fold Matthews Correlation Coefficient PPfold(20): 0.839 Fold: 0.709 Sensitivity PPfold(20): 0.721 Fold: 0.707 Positive Predictive Value PPfold(20): 0.977 Fold: 0.715 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs UNAFold Matthews Correlation Coefficient PPfold(20): 0.839 UNAFold: 0.706 Sensitivity PPfold(20): 0.721 UNAFold: 0.694 Positive Predictive Value PPfold(20): 0.977 UNAFold: 0.722 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs PknotsRG Matthews Correlation Coefficient PPfold(20): 0.839 PknotsRG: 0.689 Sensitivity PPfold(20): 0.721 PknotsRG: 0.685 Positive Predictive Value PPfold(20): 0.977 PknotsRG: 0.697 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Sfold Matthews Correlation Coefficient PPfold(20): 0.839 Sfold: 0.698 Sensitivity PPfold(20): 0.721 Sfold: 0.661 Positive Predictive Value PPfold(20): 0.977 Sfold: 0.741 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RNAalifold(seed) Matthews Correlation Coefficient PPfold(20): 0.612 RNAalifold(seed): 0.607 Sensitivity PPfold(20): 0.400 RNAalifold(seed): 0.388 Positive Predictive Value PPfold(20): 0.941 RNAalifold(seed): 0.954 Number of pairs reference - predicted secondary structure: 131 Wilcoxon single-rank test P-value: 6.58294707158e-07	+ PPfold(20) vs RNAsubopt Matthews Correlation Coefficient PPfold(20): 0.839 RNAsubopt: 0.693 Sensitivity PPfold(20): 0.721 RNAsubopt: 0.691 Positive Predictive Value PPfold(20): 0.977 RNAsubopt: 0.699 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs HotKnots Matthews Correlation Coefficient PPfold(20): 0.839 HotKnots: 0.696 Sensitivity PPfold(20): 0.721 HotKnots: 0.692 Positive Predictive Value PPfold(20): 0.977 HotKnots: 0.704 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RNAfold Matthews Correlation Coefficient PPfold(20): 0.839 RNAfold: 0.684 Sensitivity PPfold(20): 0.721 RNAfold: 0.679 Positive Predictive Value PPfold(20): 0.977 RNAfold: 0.693 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RNAshapes Matthews Correlation Coefficient PPfold(20): 0.839 RNAshapes: 0.692 Sensitivity PPfold(20): 0.721 RNAshapes: 0.686 Positive Predictive Value PPfold(20): 0.977 RNAshapes: 0.701 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RNASampler(seed) Matthews Correlation Coefficient PPfold(20): 0.690 RNASampler(seed): 0.571 Sensitivity PPfold(20): 0.547 RNASampler(seed): 0.343 Positive Predictive Value PPfold(20): 0.876 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Afold Matthews Correlation Coefficient PPfold(20): 0.764 Afold: 0.640 Sensitivity PPfold(20): 0.610 Afold: 0.628 Positive Predictive Value PPfold(20): 0.960 Afold: 0.657 Number of pairs reference - predicted secondary structure: 159 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Pknots Matthews Correlation Coefficient PPfold(20): 0.882 Pknots: 0.664 Sensitivity PPfold(20): 0.796 Pknots: 0.671 Positive Predictive Value PPfold(20): 0.979 Pknots: 0.662 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs McQFold Matthews Correlation Coefficient PPfold(20): 0.839 McQFold: 0.613 Sensitivity PPfold(20): 0.721 McQFold: 0.590 Positive Predictive Value PPfold(20): 0.977 McQFold: 0.642 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Carnac(20) Matthews Correlation Coefficient PPfold(20): 0.839 Carnac(20): 0.682 Sensitivity PPfold(20): 0.721 Carnac(20): 0.507 Positive Predictive Value PPfold(20): 0.977 Carnac(20): 0.921 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RNASLOpt Matthews Correlation Coefficient PPfold(20): 0.839 RNASLOpt: 0.641 Sensitivity PPfold(20): 0.721 RNASLOpt: 0.596 Positive Predictive Value PPfold(20): 0.977 RNASLOpt: 0.693 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Cylofold Matthews Correlation Coefficient PPfold(20): 0.837 Cylofold: 0.560 Sensitivity PPfold(20): 0.719 Cylofold: 0.546 Positive Predictive Value PPfold(20): 0.976 Cylofold: 0.579 Number of pairs reference - predicted secondary structure: 298 Wilcoxon single-rank test P-value: 3.56938820447e-08	? PPfold(20) vs Multilign(seed) Matthews Correlation Coefficient PPfold(20): 0.531 Multilign(seed): 0.334 Sensitivity PPfold(20): 0.326 Multilign(seed): 0.186 Positive Predictive Value PPfold(20): 0.875 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ PPfold(20) vs RNAwolf Matthews Correlation Coefficient PPfold(20): 0.839 RNAwolf: 0.560 Sensitivity PPfold(20): 0.721 RNAwolf: 0.565 Positive Predictive Value PPfold(20): 0.977 RNAwolf: 0.561 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs PPfold(seed) Matthews Correlation Coefficient PPfold(20): 0.588 PPfold(seed): 0.344 Sensitivity PPfold(20): 0.365 PPfold(seed): 0.128 Positive Predictive Value PPfold(20): 0.952 PPfold(seed): 0.927 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	+ PPfold(20) vs Murlet(seed) Matthews Correlation Coefficient PPfold(20): 0.664 Murlet(seed): 0.636 Sensitivity PPfold(20): 0.505 Murlet(seed): 0.428 Positive Predictive Value PPfold(20): 0.879 Murlet(seed): 0.952 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 4.83792096436e-08	+ PPfold(20) vs Alterna Matthews Correlation Coefficient PPfold(20): 0.884 Alterna: 0.618 Sensitivity PPfold(20): 0.800 Alterna: 0.626 Positive Predictive Value PPfold(20): 0.979 Alterna: 0.616 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Carnac(seed) Matthews Correlation Coefficient PPfold(20): 0.664 Carnac(seed): 0.431 Sensitivity PPfold(20): 0.485 Carnac(seed): 0.206 Positive Predictive Value PPfold(20): 0.913 Carnac(seed): 0.907 Number of pairs reference - predicted secondary structure: 68 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Vsfold4 Matthews Correlation Coefficient PPfold(20): 0.839 Vsfold4: 0.511 Sensitivity PPfold(20): 0.721 Vsfold4: 0.475 Positive Predictive Value PPfold(20): 0.977 Vsfold4: 0.556 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RSpredict(seed) Matthews Correlation Coefficient PPfold(20): 0.625 RSpredict(seed): 0.425 Sensitivity PPfold(20): 0.415 RSpredict(seed): 0.289 Positive Predictive Value PPfold(20): 0.944 RSpredict(seed): 0.633 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Vsfold5 Matthews Correlation Coefficient PPfold(20): 0.839 Vsfold5: 0.465 Sensitivity PPfold(20): 0.721 Vsfold5: 0.445 Positive Predictive Value PPfold(20): 0.977 Vsfold5: 0.492 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs RDfolder Matthews Correlation Coefficient PPfold(20): 0.884 RDfolder: 0.562 Sensitivity PPfold(20): 0.800 RDfolder: 0.517 Positive Predictive Value PPfold(20): 0.979 RDfolder: 0.618 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs MCFold Matthews Correlation Coefficient PPfold(20): 0.830 MCFold: 0.500 Sensitivity PPfold(20): 0.707 MCFold: 0.560 Positive Predictive Value PPfold(20): 0.976 MCFold: 0.454 Number of pairs reference - predicted secondary structure: 254 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs NanoFolder Matthews Correlation Coefficient PPfold(20): 0.788 NanoFolder: 0.337 Sensitivity PPfold(20): 0.639 NanoFolder: 0.392 Positive Predictive Value PPfold(20): 0.974 NanoFolder: 0.298 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(20) vs Mastr(seed) Matthews Correlation Coefficient PPfold(20): 0.662 Mastr(seed): 0.271 Sensitivity PPfold(20): 0.463 Mastr(seed): 0.091 Positive Predictive Value PPfold(20): 0.948 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 148 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNAalifold(20)	320 ContextFold vs RNAalifold(20) Matthews Correlation Coefficient ContextFold: 0.923 RNAalifold(20): 0.816 Sensitivity ContextFold: 0.898 RNAalifold(20): 0.690 Positive Predictive Value ContextFold: 0.949 RNAalifold(20): 0.966 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 TurboFold(20) vs RNAalifold(20) Matthews Correlation Coefficient TurboFold(20): 0.889 RNAalifold(20): 0.816 Sensitivity TurboFold(20): 0.861 RNAalifold(20): 0.690 Positive Predictive Value TurboFold(20): 0.919 RNAalifold(20): 0.966 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	141 CentroidAlifold(seed) vs RNAalifold(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.815 RNAalifold(20): 0.642 Sensitivity CentroidAlifold(seed): 0.743 RNAalifold(20): 0.442 Positive Predictive Value CentroidAlifold(seed): 0.897 RNAalifold(20): 0.937 Number of pairs reference - predicted secondary structure: 141 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 CentroidHomfold‑LAST vs RNAalifold(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.858 RNAalifold(20): 0.816 Sensitivity CentroidHomfold‑LAST: 0.821 RNAalifold(20): 0.690 Positive Predictive Value CentroidHomfold‑LAST: 0.900 RNAalifold(20): 0.966 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	319 PETfold_pre2.0(seed) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.885 RNAalifold(20): 0.816 Sensitivity PETfold_pre2.0(seed): 0.832 RNAalifold(20): 0.690 Positive Predictive Value PETfold_pre2.0(seed): 0.944 RNAalifold(20): 0.968 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 TurboFold(seed) vs RNAalifold(20) Matthews Correlation Coefficient TurboFold(seed): 0.880 RNAalifold(20): 0.650 Sensitivity TurboFold(seed): 0.875 RNAalifold(20): 0.461 Positive Predictive Value TurboFold(seed): 0.886 RNAalifold(20): 0.922 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.70887622364e-08	153 MXScarna(seed) vs RNAalifold(20) Matthews Correlation Coefficient MXScarna(seed): 0.792 RNAalifold(20): 0.669 Sensitivity MXScarna(seed): 0.756 RNAalifold(20): 0.476 Positive Predictive Value MXScarna(seed): 0.832 RNAalifold(20): 0.943 Number of pairs reference - predicted secondary structure: 153 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 CentroidAlifold(20) vs RNAalifold(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.849 RNAalifold(20): 0.816 Sensitivity CentroidAlifold(20): 0.754 RNAalifold(20): 0.690 Positive Predictive Value CentroidAlifold(20): 0.957 RNAalifold(20): 0.966 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 PETfold_pre2.0(20) vs RNAalifold(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 RNAalifold(20): 0.816 Sensitivity PETfold_pre2.0(20): 0.737 RNAalifold(20): 0.690 Positive Predictive Value PETfold_pre2.0(20): 0.975 RNAalifold(20): 0.966 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 MXScarna(20) vs RNAalifold(20) Matthews Correlation Coefficient MXScarna(20): 0.838 RNAalifold(20): 0.816 Sensitivity MXScarna(20): 0.791 RNAalifold(20): 0.690 Positive Predictive Value MXScarna(20): 0.891 RNAalifold(20): 0.966 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	314 PPfold(20) vs RNAalifold(20) Matthews Correlation Coefficient PPfold(20): 0.839 RNAalifold(20): 0.820 Sensitivity PPfold(20): 0.721 RNAalifold(20): 0.698 Positive Predictive Value PPfold(20): 0.977 RNAalifold(20): 0.966 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ RNAalifold(20) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(20): 0.816 RSpredict(20): 0.789 Sensitivity RNAalifold(20): 0.690 RSpredict(20): 0.693 Positive Predictive Value RNAalifold(20): 0.966 RSpredict(20): 0.901 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs IPknot Matthews Correlation Coefficient RNAalifold(20): 0.816 IPknot: 0.783 Sensitivity RNAalifold(20): 0.690 IPknot: 0.761 Positive Predictive Value RNAalifold(20): 0.966 IPknot: 0.807 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Multilign(20) Matthews Correlation Coefficient RNAalifold(20): 0.824 Multilign(20): 0.784 Sensitivity RNAalifold(20): 0.705 Multilign(20): 0.697 Positive Predictive Value RNAalifold(20): 0.966 Multilign(20): 0.885 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs CentroidFold Matthews Correlation Coefficient RNAalifold(20): 0.816 CentroidFold: 0.735 Sensitivity RNAalifold(20): 0.690 CentroidFold: 0.710 Positive Predictive Value RNAalifold(20): 0.966 CentroidFold: 0.764 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Contrafold Matthews Correlation Coefficient RNAalifold(20): 0.816 Contrafold: 0.733 Sensitivity RNAalifold(20): 0.690 Contrafold: 0.729 Positive Predictive Value RNAalifold(20): 0.966 Contrafold: 0.740 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RNASampler(20) Matthews Correlation Coefficient RNAalifold(20): 0.819 RNASampler(20): 0.770 Sensitivity RNAalifold(20): 0.695 RNASampler(20): 0.622 Positive Predictive Value RNAalifold(20): 0.966 RNASampler(20): 0.957 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Murlet(20) Matthews Correlation Coefficient RNAalifold(20): 0.816 Murlet(20): 0.750 Sensitivity RNAalifold(20): 0.690 Murlet(20): 0.619 Positive Predictive Value RNAalifold(20): 0.968 Murlet(20): 0.913 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CMfinder(seed) vs RNAalifold(20) Matthews Correlation Coefficient CMfinder(seed): 0.736 RNAalifold(20): 0.620 Sensitivity CMfinder(seed): 0.607 RNAalifold(20): 0.466 Positive Predictive Value CMfinder(seed): 0.898 RNAalifold(20): 0.832 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ RNAalifold(20) vs MaxExpect Matthews Correlation Coefficient RNAalifold(20): 0.816 MaxExpect: 0.711 Sensitivity RNAalifold(20): 0.690 MaxExpect: 0.701 Positive Predictive Value RNAalifold(20): 0.966 MaxExpect: 0.725 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs CMfinder(20) Matthews Correlation Coefficient RNAalifold(20): 0.820 CMfinder(20): 0.735 Sensitivity RNAalifold(20): 0.698 CMfinder(20): 0.603 Positive Predictive Value RNAalifold(20): 0.966 CMfinder(20): 0.899 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs CRWrnafold Matthews Correlation Coefficient RNAalifold(20): 0.816 CRWrnafold: 0.783 Sensitivity RNAalifold(20): 0.690 CRWrnafold: 0.771 Positive Predictive Value RNAalifold(20): 0.966 CRWrnafold: 0.798 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs ProbKnot Matthews Correlation Coefficient RNAalifold(20): 0.816 ProbKnot: 0.707 Sensitivity RNAalifold(20): 0.690 ProbKnot: 0.702 Positive Predictive Value RNAalifold(20): 0.966 ProbKnot: 0.716 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(20): 0.816 Mastr(20): 0.708 Sensitivity RNAalifold(20): 0.690 Mastr(20): 0.635 Positive Predictive Value RNAalifold(20): 0.966 Mastr(20): 0.793 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Fold Matthews Correlation Coefficient RNAalifold(20): 0.816 Fold: 0.712 Sensitivity RNAalifold(20): 0.690 Fold: 0.710 Positive Predictive Value RNAalifold(20): 0.966 Fold: 0.717 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs UNAFold Matthews Correlation Coefficient RNAalifold(20): 0.816 UNAFold: 0.708 Sensitivity RNAalifold(20): 0.690 UNAFold: 0.696 Positive Predictive Value RNAalifold(20): 0.966 UNAFold: 0.723 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs PknotsRG Matthews Correlation Coefficient RNAalifold(20): 0.816 PknotsRG: 0.691 Sensitivity RNAalifold(20): 0.690 PknotsRG: 0.687 Positive Predictive Value RNAalifold(20): 0.966 PknotsRG: 0.699 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Sfold Matthews Correlation Coefficient RNAalifold(20): 0.816 Sfold: 0.698 Sensitivity RNAalifold(20): 0.690 Sfold: 0.662 Positive Predictive Value RNAalifold(20): 0.966 Sfold: 0.740 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.630 RNAalifold(seed): 0.604 Sensitivity RNAalifold(20): 0.427 RNAalifold(seed): 0.383 Positive Predictive Value RNAalifold(20): 0.934 RNAalifold(seed): 0.956 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RNAsubopt Matthews Correlation Coefficient RNAalifold(20): 0.816 RNAsubopt: 0.694 Sensitivity RNAalifold(20): 0.690 RNAsubopt: 0.693 Positive Predictive Value RNAalifold(20): 0.966 RNAsubopt: 0.700 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs HotKnots Matthews Correlation Coefficient RNAalifold(20): 0.816 HotKnots: 0.698 Sensitivity RNAalifold(20): 0.690 HotKnots: 0.695 Positive Predictive Value RNAalifold(20): 0.966 HotKnots: 0.705 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RNAfold Matthews Correlation Coefficient RNAalifold(20): 0.816 RNAfold: 0.686 Sensitivity RNAalifold(20): 0.690 RNAfold: 0.681 Positive Predictive Value RNAalifold(20): 0.966 RNAfold: 0.695 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RNAshapes Matthews Correlation Coefficient RNAalifold(20): 0.816 RNAshapes: 0.693 Sensitivity RNAalifold(20): 0.690 RNAshapes: 0.687 Positive Predictive Value RNAalifold(20): 0.966 RNAshapes: 0.702 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RNASampler(seed) Matthews Correlation Coefficient RNAalifold(20): 0.659 RNASampler(seed): 0.571 Sensitivity RNAalifold(20): 0.511 RNASampler(seed): 0.343 Positive Predictive Value RNAalifold(20): 0.857 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Afold Matthews Correlation Coefficient RNAalifold(20): 0.741 Afold: 0.643 Sensitivity RNAalifold(20): 0.580 Afold: 0.632 Positive Predictive Value RNAalifold(20): 0.950 Afold: 0.659 Number of pairs reference - predicted secondary structure: 163 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Pknots Matthews Correlation Coefficient RNAalifold(20): 0.881 Pknots: 0.655 Sensitivity RNAalifold(20): 0.794 Pknots: 0.662 Positive Predictive Value RNAalifold(20): 0.980 Pknots: 0.653 Number of pairs reference - predicted secondary structure: 212 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs McQFold Matthews Correlation Coefficient RNAalifold(20): 0.816 McQFold: 0.610 Sensitivity RNAalifold(20): 0.690 McQFold: 0.587 Positive Predictive Value RNAalifold(20): 0.966 McQFold: 0.639 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(20): 0.816 Carnac(20): 0.675 Sensitivity RNAalifold(20): 0.690 Carnac(20): 0.500 Positive Predictive Value RNAalifold(20): 0.966 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(20): 0.816 RNASLOpt: 0.638 Sensitivity RNAalifold(20): 0.690 RNASLOpt: 0.594 Positive Predictive Value RNAalifold(20): 0.966 RNASLOpt: 0.690 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Cylofold Matthews Correlation Coefficient RNAalifold(20): 0.816 Cylofold: 0.557 Sensitivity RNAalifold(20): 0.690 Cylofold: 0.543 Positive Predictive Value RNAalifold(20): 0.968 Cylofold: 0.577 Number of pairs reference - predicted secondary structure: 304 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNAalifold(20) vs Multilign(seed) Matthews Correlation Coefficient RNAalifold(20): 0.568 Multilign(seed): 0.334 Sensitivity RNAalifold(20): 0.326 Multilign(seed): 0.186 Positive Predictive Value RNAalifold(20): 1.000 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ RNAalifold(20) vs RNAwolf Matthews Correlation Coefficient RNAalifold(20): 0.816 RNAwolf: 0.561 Sensitivity RNAalifold(20): 0.690 RNAwolf: 0.565 Positive Predictive Value RNAalifold(20): 0.966 RNAwolf: 0.561 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs PPfold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.667 PPfold(seed): 0.344 Sensitivity RNAalifold(20): 0.471 PPfold(seed): 0.128 Positive Predictive Value RNAalifold(20): 0.949 PPfold(seed): 0.927 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.1503931209e-08	= RNAalifold(20) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(20): 0.637 Murlet(seed): 0.636 Sensitivity RNAalifold(20): 0.475 Murlet(seed): 0.428 Positive Predictive Value RNAalifold(20): 0.861 Murlet(seed): 0.952 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 0.667107250991	+ RNAalifold(20) vs Alterna Matthews Correlation Coefficient RNAalifold(20): 0.883 Alterna: 0.618 Sensitivity RNAalifold(20): 0.795 Alterna: 0.626 Positive Predictive Value RNAalifold(20): 0.982 Alterna: 0.616 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(20): 0.671 Carnac(seed): 0.431 Sensitivity RNAalifold(20): 0.496 Carnac(seed): 0.206 Positive Predictive Value RNAalifold(20): 0.911 Carnac(seed): 0.907 Number of pairs reference - predicted secondary structure: 68 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(20): 0.816 Vsfold4: 0.502 Sensitivity RNAalifold(20): 0.690 Vsfold4: 0.466 Positive Predictive Value RNAalifold(20): 0.966 Vsfold4: 0.546 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(20): 0.642 RSpredict(seed): 0.414 Sensitivity RNAalifold(20): 0.442 RSpredict(seed): 0.279 Positive Predictive Value RNAalifold(20): 0.937 RSpredict(seed): 0.622 Number of pairs reference - predicted secondary structure: 141 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(20): 0.816 Vsfold5: 0.457 Sensitivity RNAalifold(20): 0.690 Vsfold5: 0.437 Positive Predictive Value RNAalifold(20): 0.966 Vsfold5: 0.484 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs RDfolder Matthews Correlation Coefficient RNAalifold(20): 0.883 RDfolder: 0.556 Sensitivity RNAalifold(20): 0.795 RDfolder: 0.511 Positive Predictive Value RNAalifold(20): 0.982 RDfolder: 0.611 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs MCFold Matthews Correlation Coefficient RNAalifold(20): 0.817 MCFold: 0.500 Sensitivity RNAalifold(20): 0.689 MCFold: 0.559 Positive Predictive Value RNAalifold(20): 0.970 MCFold: 0.453 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs NanoFolder Matthews Correlation Coefficient RNAalifold(20): 0.767 NanoFolder: 0.337 Sensitivity RNAalifold(20): 0.614 NanoFolder: 0.391 Positive Predictive Value RNAalifold(20): 0.959 NanoFolder: 0.298 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(20) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(20): 0.671 Mastr(seed): 0.265 Sensitivity RNAalifold(20): 0.478 Mastr(seed): 0.087 Positive Predictive Value RNAalifold(20): 0.944 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 154 Wilcoxon single-rank test P-value: 3.56938820447e-08
RSpredict(20)	320 ContextFold vs RSpredict(20) Matthews Correlation Coefficient ContextFold: 0.923 RSpredict(20): 0.789 Sensitivity ContextFold: 0.898 RSpredict(20): 0.693 Positive Predictive Value ContextFold: 0.949 RSpredict(20): 0.901 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 TurboFold(20) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(20): 0.889 RSpredict(20): 0.789 Sensitivity TurboFold(20): 0.861 RSpredict(20): 0.693 Positive Predictive Value TurboFold(20): 0.919 RSpredict(20): 0.901 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	141 CentroidAlifold(seed) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.815 RSpredict(20): 0.716 Sensitivity CentroidAlifold(seed): 0.743 RSpredict(20): 0.594 Positive Predictive Value CentroidAlifold(seed): 0.897 RSpredict(20): 0.866 Number of pairs reference - predicted secondary structure: 141 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 CentroidHomfold‑LAST vs RSpredict(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.858 RSpredict(20): 0.789 Sensitivity CentroidHomfold‑LAST: 0.821 RSpredict(20): 0.693 Positive Predictive Value CentroidHomfold‑LAST: 0.900 RSpredict(20): 0.901 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	319 PETfold_pre2.0(seed) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.885 RSpredict(20): 0.789 Sensitivity PETfold_pre2.0(seed): 0.832 RSpredict(20): 0.693 Positive Predictive Value PETfold_pre2.0(seed): 0.944 RSpredict(20): 0.901 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 TurboFold(seed) vs RSpredict(20) Matthews Correlation Coefficient TurboFold(seed): 0.880 RSpredict(20): 0.788 Sensitivity TurboFold(seed): 0.875 RSpredict(20): 0.679 Positive Predictive Value TurboFold(seed): 0.886 RSpredict(20): 0.917 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.76499031155e-08	153 MXScarna(seed) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(seed): 0.792 RSpredict(20): 0.726 Sensitivity MXScarna(seed): 0.756 RSpredict(20): 0.606 Positive Predictive Value MXScarna(seed): 0.832 RSpredict(20): 0.873 Number of pairs reference - predicted secondary structure: 153 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 CentroidAlifold(20) vs RSpredict(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.849 RSpredict(20): 0.789 Sensitivity CentroidAlifold(20): 0.754 RSpredict(20): 0.693 Positive Predictive Value CentroidAlifold(20): 0.957 RSpredict(20): 0.901 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 PETfold_pre2.0(20) vs RSpredict(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 RSpredict(20): 0.789 Sensitivity PETfold_pre2.0(20): 0.737 RSpredict(20): 0.693 Positive Predictive Value PETfold_pre2.0(20): 0.975 RSpredict(20): 0.901 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 MXScarna(20) vs RSpredict(20) Matthews Correlation Coefficient MXScarna(20): 0.838 RSpredict(20): 0.789 Sensitivity MXScarna(20): 0.791 RSpredict(20): 0.693 Positive Predictive Value MXScarna(20): 0.891 RSpredict(20): 0.901 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	314 PPfold(20) vs RSpredict(20) Matthews Correlation Coefficient PPfold(20): 0.839 RSpredict(20): 0.796 Sensitivity PPfold(20): 0.721 RSpredict(20): 0.704 Positive Predictive Value PPfold(20): 0.977 RSpredict(20): 0.902 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RNAalifold(20) vs RSpredict(20) Matthews Correlation Coefficient RNAalifold(20): 0.816 RSpredict(20): 0.789 Sensitivity RNAalifold(20): 0.690 RSpredict(20): 0.693 Positive Predictive Value RNAalifold(20): 0.966 RSpredict(20): 0.901 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ RSpredict(20) vs IPknot Matthews Correlation Coefficient RSpredict(20): 0.789 IPknot: 0.783 Sensitivity RSpredict(20): 0.693 IPknot: 0.761 Positive Predictive Value RSpredict(20): 0.901 IPknot: 0.807 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 2.12176083234e-07	+ RSpredict(20) vs Multilign(20) Matthews Correlation Coefficient RSpredict(20): 0.793 Multilign(20): 0.784 Sensitivity RSpredict(20): 0.698 Multilign(20): 0.697 Positive Predictive Value RSpredict(20): 0.903 Multilign(20): 0.885 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 6.53888633552e-08	+ RSpredict(20) vs CentroidFold Matthews Correlation Coefficient RSpredict(20): 0.789 CentroidFold: 0.735 Sensitivity RSpredict(20): 0.693 CentroidFold: 0.710 Positive Predictive Value RSpredict(20): 0.901 CentroidFold: 0.764 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs Contrafold Matthews Correlation Coefficient RSpredict(20): 0.789 Contrafold: 0.733 Sensitivity RSpredict(20): 0.693 Contrafold: 0.729 Positive Predictive Value RSpredict(20): 0.901 Contrafold: 0.740 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs RNASampler(20) Matthews Correlation Coefficient RSpredict(20): 0.793 RNASampler(20): 0.770 Sensitivity RSpredict(20): 0.700 RNASampler(20): 0.622 Positive Predictive Value RSpredict(20): 0.902 RNASampler(20): 0.957 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs Murlet(20) Matthews Correlation Coefficient RSpredict(20): 0.789 Murlet(20): 0.750 Sensitivity RSpredict(20): 0.693 Murlet(20): 0.619 Positive Predictive Value RSpredict(20): 0.901 Murlet(20): 0.913 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	= CMfinder(seed) vs RSpredict(20) Matthews Correlation Coefficient CMfinder(seed): 0.736 RSpredict(20): 0.729 Sensitivity CMfinder(seed): 0.607 RSpredict(20): 0.656 Positive Predictive Value CMfinder(seed): 0.898 RSpredict(20): 0.816 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 0.00531619474363	+ RSpredict(20) vs MaxExpect Matthews Correlation Coefficient RSpredict(20): 0.789 MaxExpect: 0.711 Sensitivity RSpredict(20): 0.693 MaxExpect: 0.701 Positive Predictive Value RSpredict(20): 0.901 MaxExpect: 0.725 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs CMfinder(20) Matthews Correlation Coefficient RSpredict(20): 0.796 CMfinder(20): 0.735 Sensitivity RSpredict(20): 0.705 CMfinder(20): 0.603 Positive Predictive Value RSpredict(20): 0.902 CMfinder(20): 0.899 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs CRWrnafold Matthews Correlation Coefficient RSpredict(20): 0.789 CRWrnafold: 0.783 Sensitivity RSpredict(20): 0.693 CRWrnafold: 0.771 Positive Predictive Value RSpredict(20): 0.901 CRWrnafold: 0.798 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 4.98094999346e-07	+ RSpredict(20) vs ProbKnot Matthews Correlation Coefficient RSpredict(20): 0.789 ProbKnot: 0.707 Sensitivity RSpredict(20): 0.693 ProbKnot: 0.702 Positive Predictive Value RSpredict(20): 0.901 ProbKnot: 0.716 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs Mastr(20) Matthews Correlation Coefficient RSpredict(20): 0.789 Mastr(20): 0.708 Sensitivity RSpredict(20): 0.693 Mastr(20): 0.635 Positive Predictive Value RSpredict(20): 0.901 Mastr(20): 0.793 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs Fold Matthews Correlation Coefficient RSpredict(20): 0.789 Fold: 0.712 Sensitivity RSpredict(20): 0.693 Fold: 0.710 Positive Predictive Value RSpredict(20): 0.901 Fold: 0.717 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs UNAFold Matthews Correlation Coefficient RSpredict(20): 0.789 UNAFold: 0.708 Sensitivity RSpredict(20): 0.693 UNAFold: 0.696 Positive Predictive Value RSpredict(20): 0.901 UNAFold: 0.723 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs PknotsRG Matthews Correlation Coefficient RSpredict(20): 0.789 PknotsRG: 0.691 Sensitivity RSpredict(20): 0.693 PknotsRG: 0.687 Positive Predictive Value RSpredict(20): 0.901 PknotsRG: 0.699 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs Sfold Matthews Correlation Coefficient RSpredict(20): 0.789 Sfold: 0.698 Sensitivity RSpredict(20): 0.693 Sfold: 0.662 Positive Predictive Value RSpredict(20): 0.901 Sfold: 0.740 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs RNAalifold(seed) Matthews Correlation Coefficient RSpredict(20): 0.710 RNAalifold(seed): 0.604 Sensitivity RSpredict(20): 0.586 RNAalifold(seed): 0.383 Positive Predictive Value RSpredict(20): 0.864 RNAalifold(seed): 0.956 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs RNAsubopt Matthews Correlation Coefficient RSpredict(20): 0.789 RNAsubopt: 0.694 Sensitivity RSpredict(20): 0.693 RNAsubopt: 0.693 Positive Predictive Value RSpredict(20): 0.901 RNAsubopt: 0.700 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs HotKnots Matthews Correlation Coefficient RSpredict(20): 0.789 HotKnots: 0.698 Sensitivity RSpredict(20): 0.693 HotKnots: 0.695 Positive Predictive Value RSpredict(20): 0.901 HotKnots: 0.705 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs RNAfold Matthews Correlation Coefficient RSpredict(20): 0.789 RNAfold: 0.686 Sensitivity RSpredict(20): 0.693 RNAfold: 0.681 Positive Predictive Value RSpredict(20): 0.901 RNAfold: 0.695 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs RNAshapes Matthews Correlation Coefficient RSpredict(20): 0.789 RNAshapes: 0.693 Sensitivity RSpredict(20): 0.693 RNAshapes: 0.687 Positive Predictive Value RSpredict(20): 0.901 RNAshapes: 0.702 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs RNASampler(seed) Matthews Correlation Coefficient RSpredict(20): 0.753 RNASampler(seed): 0.571 Sensitivity RSpredict(20): 0.684 RNASampler(seed): 0.343 Positive Predictive Value RSpredict(20): 0.833 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RSpredict(20) vs Afold Matthews Correlation Coefficient RSpredict(20): 0.775 Afold: 0.643 Sensitivity RSpredict(20): 0.677 Afold: 0.632 Positive Predictive Value RSpredict(20): 0.890 Afold: 0.659 Number of pairs reference - predicted secondary structure: 163 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs Pknots Matthews Correlation Coefficient RSpredict(20): 0.821 Pknots: 0.655 Sensitivity RSpredict(20): 0.738 Pknots: 0.662 Positive Predictive Value RSpredict(20): 0.915 Pknots: 0.653 Number of pairs reference - predicted secondary structure: 212 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs McQFold Matthews Correlation Coefficient RSpredict(20): 0.789 McQFold: 0.610 Sensitivity RSpredict(20): 0.693 McQFold: 0.587 Positive Predictive Value RSpredict(20): 0.901 McQFold: 0.639 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs Carnac(20) Matthews Correlation Coefficient RSpredict(20): 0.789 Carnac(20): 0.675 Sensitivity RSpredict(20): 0.693 Carnac(20): 0.500 Positive Predictive Value RSpredict(20): 0.901 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs RNASLOpt Matthews Correlation Coefficient RSpredict(20): 0.789 RNASLOpt: 0.638 Sensitivity RSpredict(20): 0.693 RNASLOpt: 0.594 Positive Predictive Value RSpredict(20): 0.901 RNASLOpt: 0.690 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs Cylofold Matthews Correlation Coefficient RSpredict(20): 0.794 Cylofold: 0.557 Sensitivity RSpredict(20): 0.700 Cylofold: 0.543 Positive Predictive Value RSpredict(20): 0.903 Cylofold: 0.577 Number of pairs reference - predicted secondary structure: 304 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RSpredict(20) vs Multilign(seed) Matthews Correlation Coefficient RSpredict(20): 0.739 Multilign(seed): 0.334 Sensitivity RSpredict(20): 0.698 Multilign(seed): 0.186 Positive Predictive Value RSpredict(20): 0.789 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ RSpredict(20) vs RNAwolf Matthews Correlation Coefficient RSpredict(20): 0.789 RNAwolf: 0.561 Sensitivity RSpredict(20): 0.693 RNAwolf: 0.565 Positive Predictive Value RSpredict(20): 0.901 RNAwolf: 0.561 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs PPfold(seed) Matthews Correlation Coefficient RSpredict(20): 0.782 PPfold(seed): 0.344 Sensitivity RSpredict(20): 0.666 PPfold(seed): 0.128 Positive Predictive Value RSpredict(20): 0.923 PPfold(seed): 0.927 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 4.98172311752e-08	+ RSpredict(20) vs Murlet(seed) Matthews Correlation Coefficient RSpredict(20): 0.742 Murlet(seed): 0.636 Sensitivity RSpredict(20): 0.662 Murlet(seed): 0.428 Positive Predictive Value RSpredict(20): 0.838 Murlet(seed): 0.952 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs Alterna Matthews Correlation Coefficient RSpredict(20): 0.821 Alterna: 0.618 Sensitivity RSpredict(20): 0.738 Alterna: 0.626 Positive Predictive Value RSpredict(20): 0.917 Alterna: 0.616 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(20): 0.759 Carnac(seed): 0.431 Sensitivity RSpredict(20): 0.662 Carnac(seed): 0.206 Positive Predictive Value RSpredict(20): 0.873 Carnac(seed): 0.907 Number of pairs reference - predicted secondary structure: 68 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs Vsfold4 Matthews Correlation Coefficient RSpredict(20): 0.789 Vsfold4: 0.502 Sensitivity RSpredict(20): 0.693 Vsfold4: 0.466 Positive Predictive Value RSpredict(20): 0.901 Vsfold4: 0.546 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs RSpredict(seed) Matthews Correlation Coefficient RSpredict(20): 0.716 RSpredict(seed): 0.414 Sensitivity RSpredict(20): 0.594 RSpredict(seed): 0.279 Positive Predictive Value RSpredict(20): 0.866 RSpredict(seed): 0.622 Number of pairs reference - predicted secondary structure: 141 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs Vsfold5 Matthews Correlation Coefficient RSpredict(20): 0.789 Vsfold5: 0.457 Sensitivity RSpredict(20): 0.693 Vsfold5: 0.437 Positive Predictive Value RSpredict(20): 0.901 Vsfold5: 0.484 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs RDfolder Matthews Correlation Coefficient RSpredict(20): 0.821 RDfolder: 0.556 Sensitivity RSpredict(20): 0.738 RDfolder: 0.511 Positive Predictive Value RSpredict(20): 0.917 RDfolder: 0.611 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs MCFold Matthews Correlation Coefficient RSpredict(20): 0.789 MCFold: 0.500 Sensitivity RSpredict(20): 0.690 MCFold: 0.559 Positive Predictive Value RSpredict(20): 0.905 MCFold: 0.453 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs NanoFolder Matthews Correlation Coefficient RSpredict(20): 0.748 NanoFolder: 0.337 Sensitivity RSpredict(20): 0.635 NanoFolder: 0.391 Positive Predictive Value RSpredict(20): 0.886 NanoFolder: 0.298 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(20) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(20): 0.723 Mastr(seed): 0.265 Sensitivity RSpredict(20): 0.602 Mastr(seed): 0.087 Positive Predictive Value RSpredict(20): 0.871 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 154 Wilcoxon single-rank test P-value: 3.56938820447e-08
IPknot	882 ContextFold vs IPknot Matthews Correlation Coefficient ContextFold: 0.779 IPknot: 0.694 Sensitivity ContextFold: 0.741 IPknot: 0.661 Positive Predictive Value ContextFold: 0.823 IPknot: 0.733 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 TurboFold(20) vs IPknot Matthews Correlation Coefficient TurboFold(20): 0.889 IPknot: 0.783 Sensitivity TurboFold(20): 0.861 IPknot: 0.761 Positive Predictive Value TurboFold(20): 0.919 IPknot: 0.807 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	216 CentroidAlifold(seed) vs IPknot Matthews Correlation Coefficient CentroidAlifold(seed): 0.790 IPknot: 0.733 Sensitivity CentroidAlifold(seed): 0.699 IPknot: 0.708 Positive Predictive Value CentroidAlifold(seed): 0.896 IPknot: 0.762 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 CentroidHomfold‑LAST vs IPknot Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.736 IPknot: 0.694 Sensitivity CentroidHomfold‑LAST: 0.665 IPknot: 0.661 Positive Predictive Value CentroidHomfold‑LAST: 0.818 IPknot: 0.733 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	498 PETfold_pre2.0(seed) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.879 IPknot: 0.761 Sensitivity PETfold_pre2.0(seed): 0.825 IPknot: 0.737 Positive Predictive Value PETfold_pre2.0(seed): 0.938 IPknot: 0.788 Number of pairs reference - predicted secondary structure: 498 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 TurboFold(seed) vs IPknot Matthews Correlation Coefficient TurboFold(seed): 0.798 IPknot: 0.781 Sensitivity TurboFold(seed): 0.766 IPknot: 0.756 Positive Predictive Value TurboFold(seed): 0.835 IPknot: 0.811 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	233 MXScarna(seed) vs IPknot Matthews Correlation Coefficient MXScarna(seed): 0.750 IPknot: 0.735 Sensitivity MXScarna(seed): 0.712 IPknot: 0.710 Positive Predictive Value MXScarna(seed): 0.793 IPknot: 0.764 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 CentroidAlifold(20) vs IPknot Matthews Correlation Coefficient CentroidAlifold(20): 0.849 IPknot: 0.783 Sensitivity CentroidAlifold(20): 0.754 IPknot: 0.761 Positive Predictive Value CentroidAlifold(20): 0.957 IPknot: 0.807 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 PETfold_pre2.0(20) vs IPknot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 IPknot: 0.783 Sensitivity PETfold_pre2.0(20): 0.737 IPknot: 0.761 Positive Predictive Value PETfold_pre2.0(20): 0.975 IPknot: 0.807 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 MXScarna(20) vs IPknot Matthews Correlation Coefficient MXScarna(20): 0.838 IPknot: 0.783 Sensitivity MXScarna(20): 0.791 IPknot: 0.761 Positive Predictive Value MXScarna(20): 0.891 IPknot: 0.807 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	314 PPfold(20) vs IPknot Matthews Correlation Coefficient PPfold(20): 0.839 IPknot: 0.782 Sensitivity PPfold(20): 0.721 IPknot: 0.760 Positive Predictive Value PPfold(20): 0.977 IPknot: 0.807 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RNAalifold(20) vs IPknot Matthews Correlation Coefficient RNAalifold(20): 0.816 IPknot: 0.783 Sensitivity RNAalifold(20): 0.690 IPknot: 0.761 Positive Predictive Value RNAalifold(20): 0.966 IPknot: 0.807 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RSpredict(20) vs IPknot Matthews Correlation Coefficient RSpredict(20): 0.789 IPknot: 0.783 Sensitivity RSpredict(20): 0.693 IPknot: 0.761 Positive Predictive Value RSpredict(20): 0.901 IPknot: 0.807 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 2.12176083234e-07		- Multilign(20) vs IPknot Matthews Correlation Coefficient Multilign(20): 0.784 IPknot: 0.779 Sensitivity Multilign(20): 0.697 IPknot: 0.757 Positive Predictive Value Multilign(20): 0.885 IPknot: 0.804 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 2.28033735003e-07	+ IPknot vs CentroidFold Matthews Correlation Coefficient IPknot: 0.694 CentroidFold: 0.645 Sensitivity IPknot: 0.661 CentroidFold: 0.612 Positive Predictive Value IPknot: 0.733 CentroidFold: 0.684 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Contrafold Matthews Correlation Coefficient IPknot: 0.694 Contrafold: 0.643 Sensitivity IPknot: 0.661 Contrafold: 0.634 Positive Predictive Value IPknot: 0.733 Contrafold: 0.657 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNASampler(20) Matthews Correlation Coefficient IPknot: 0.785 RNASampler(20): 0.770 Sensitivity IPknot: 0.763 RNASampler(20): 0.622 Positive Predictive Value IPknot: 0.810 RNASampler(20): 0.957 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Murlet(20) Matthews Correlation Coefficient IPknot: 0.783 Murlet(20): 0.750 Sensitivity IPknot: 0.762 Murlet(20): 0.619 Positive Predictive Value IPknot: 0.808 Murlet(20): 0.913 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs CMfinder(seed) Matthews Correlation Coefficient IPknot: 0.617 CMfinder(seed): 0.571 Sensitivity IPknot: 0.554 CMfinder(seed): 0.439 Positive Predictive Value IPknot: 0.692 CMfinder(seed): 0.747 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs MaxExpect Matthews Correlation Coefficient IPknot: 0.694 MaxExpect: 0.633 Sensitivity IPknot: 0.661 MaxExpect: 0.617 Positive Predictive Value IPknot: 0.733 MaxExpect: 0.654 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs CMfinder(20) Matthews Correlation Coefficient IPknot: 0.781 CMfinder(20): 0.735 Sensitivity IPknot: 0.760 CMfinder(20): 0.603 Positive Predictive Value IPknot: 0.806 CMfinder(20): 0.899 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs CRWrnafold Matthews Correlation Coefficient IPknot: 0.694 CRWrnafold: 0.630 Sensitivity IPknot: 0.661 CRWrnafold: 0.618 Positive Predictive Value IPknot: 0.733 CRWrnafold: 0.648 Number of pairs reference - predicted secondary structure: 881 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs ProbKnot Matthews Correlation Coefficient IPknot: 0.694 ProbKnot: 0.630 Sensitivity IPknot: 0.661 ProbKnot: 0.622 Positive Predictive Value IPknot: 0.733 ProbKnot: 0.644 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Mastr(20) Matthews Correlation Coefficient IPknot: 0.783 Mastr(20): 0.708 Sensitivity IPknot: 0.761 Mastr(20): 0.635 Positive Predictive Value IPknot: 0.807 Mastr(20): 0.793 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Fold Matthews Correlation Coefficient IPknot: 0.694 Fold: 0.628 Sensitivity IPknot: 0.661 Fold: 0.620 Positive Predictive Value IPknot: 0.733 Fold: 0.641 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs UNAFold Matthews Correlation Coefficient IPknot: 0.694 UNAFold: 0.620 Sensitivity IPknot: 0.661 UNAFold: 0.605 Positive Predictive Value IPknot: 0.733 UNAFold: 0.639 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs PknotsRG Matthews Correlation Coefficient IPknot: 0.694 PknotsRG: 0.617 Sensitivity IPknot: 0.661 PknotsRG: 0.610 Positive Predictive Value IPknot: 0.733 PknotsRG: 0.630 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Sfold Matthews Correlation Coefficient IPknot: 0.694 Sfold: 0.618 Sensitivity IPknot: 0.661 Sfold: 0.581 Positive Predictive Value IPknot: 0.733 Sfold: 0.663 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNAalifold(seed) Matthews Correlation Coefficient IPknot: 0.734 RNAalifold(seed): 0.610 Sensitivity IPknot: 0.708 RNAalifold(seed): 0.404 Positive Predictive Value IPknot: 0.764 RNAalifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNAsubopt Matthews Correlation Coefficient IPknot: 0.694 RNAsubopt: 0.615 Sensitivity IPknot: 0.661 RNAsubopt: 0.609 Positive Predictive Value IPknot: 0.733 RNAsubopt: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs HotKnots Matthews Correlation Coefficient IPknot: 0.692 HotKnots: 0.613 Sensitivity IPknot: 0.659 HotKnots: 0.607 Positive Predictive Value IPknot: 0.730 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 875 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNAfold Matthews Correlation Coefficient IPknot: 0.694 RNAfold: 0.612 Sensitivity IPknot: 0.661 RNAfold: 0.604 Positive Predictive Value IPknot: 0.733 RNAfold: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNAshapes Matthews Correlation Coefficient IPknot: 0.694 RNAshapes: 0.612 Sensitivity IPknot: 0.661 RNAshapes: 0.602 Positive Predictive Value IPknot: 0.733 RNAshapes: 0.628 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNASampler(seed) Matthews Correlation Coefficient IPknot: 0.635 RNASampler(seed): 0.557 Sensitivity IPknot: 0.572 RNASampler(seed): 0.389 Positive Predictive Value IPknot: 0.709 RNASampler(seed): 0.802 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Afold Matthews Correlation Coefficient IPknot: 0.669 Afold: 0.558 Sensitivity IPknot: 0.626 Afold: 0.541 Positive Predictive Value IPknot: 0.719 Afold: 0.582 Number of pairs reference - predicted secondary structure: 530 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Pknots Matthews Correlation Coefficient IPknot: 0.687 Pknots: 0.606 Sensitivity IPknot: 0.652 Pknots: 0.595 Positive Predictive Value IPknot: 0.729 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs McQFold Matthews Correlation Coefficient IPknot: 0.694 McQFold: 0.583 Sensitivity IPknot: 0.661 McQFold: 0.557 Positive Predictive Value IPknot: 0.733 McQFold: 0.616 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Carnac(20) Matthews Correlation Coefficient IPknot: 0.783 Carnac(20): 0.675 Sensitivity IPknot: 0.761 Carnac(20): 0.500 Positive Predictive Value IPknot: 0.807 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RNASLOpt Matthews Correlation Coefficient IPknot: 0.694 RNASLOpt: 0.562 Sensitivity IPknot: 0.661 RNASLOpt: 0.521 Positive Predictive Value IPknot: 0.733 RNASLOpt: 0.613 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Cylofold Matthews Correlation Coefficient IPknot: 0.719 Cylofold: 0.577 Sensitivity IPknot: 0.687 Cylofold: 0.554 Positive Predictive Value IPknot: 0.757 Cylofold: 0.608 Number of pairs reference - predicted secondary structure: 796 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Multilign(seed) Matthews Correlation Coefficient IPknot: 0.581 Multilign(seed): 0.485 Sensitivity IPknot: 0.502 Multilign(seed): 0.386 Positive Predictive Value IPknot: 0.679 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.16131455263e-08	+ IPknot vs RNAwolf Matthews Correlation Coefficient IPknot: 0.694 RNAwolf: 0.518 Sensitivity IPknot: 0.661 RNAwolf: 0.523 Positive Predictive Value IPknot: 0.733 RNAwolf: 0.520 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs PPfold(seed) Matthews Correlation Coefficient IPknot: 0.802 PPfold(seed): 0.380 Sensitivity IPknot: 0.780 PPfold(seed): 0.170 Positive Predictive Value IPknot: 0.827 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Murlet(seed) Matthews Correlation Coefficient IPknot: 0.662 Murlet(seed): 0.468 Sensitivity IPknot: 0.604 Murlet(seed): 0.266 Positive Predictive Value IPknot: 0.730 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Alterna Matthews Correlation Coefficient IPknot: 0.689 Alterna: 0.552 Sensitivity IPknot: 0.655 Alterna: 0.547 Positive Predictive Value IPknot: 0.731 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Carnac(seed) Matthews Correlation Coefficient IPknot: 0.713 Carnac(seed): 0.415 Sensitivity IPknot: 0.668 Carnac(seed): 0.196 Positive Predictive Value IPknot: 0.764 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Vsfold4 Matthews Correlation Coefficient IPknot: 0.694 Vsfold4: 0.487 Sensitivity IPknot: 0.661 Vsfold4: 0.447 Positive Predictive Value IPknot: 0.733 Vsfold4: 0.537 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RSpredict(seed) Matthews Correlation Coefficient IPknot: 0.733 RSpredict(seed): 0.373 Sensitivity IPknot: 0.708 RSpredict(seed): 0.251 Positive Predictive Value IPknot: 0.762 RSpredict(seed): 0.562 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Vsfold5 Matthews Correlation Coefficient IPknot: 0.694 Vsfold5: 0.477 Sensitivity IPknot: 0.661 Vsfold5: 0.450 Positive Predictive Value IPknot: 0.733 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs RDfolder Matthews Correlation Coefficient IPknot: 0.689 RDfolder: 0.520 Sensitivity IPknot: 0.655 RDfolder: 0.464 Positive Predictive Value IPknot: 0.731 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs MCFold Matthews Correlation Coefficient IPknot: 0.689 MCFold: 0.473 Sensitivity IPknot: 0.654 MCFold: 0.524 Positive Predictive Value IPknot: 0.730 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs NanoFolder Matthews Correlation Coefficient IPknot: 0.724 NanoFolder: 0.335 Sensitivity IPknot: 0.694 NanoFolder: 0.384 Positive Predictive Value IPknot: 0.759 NanoFolder: 0.301 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ IPknot vs Mastr(seed) Matthews Correlation Coefficient IPknot: 0.736 Mastr(seed): 0.263 Sensitivity IPknot: 0.711 Mastr(seed): 0.089 Positive Predictive Value IPknot: 0.764 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08
Multilign(20)	311 ContextFold vs Multilign(20) Matthews Correlation Coefficient ContextFold: 0.921 Multilign(20): 0.784 Sensitivity ContextFold: 0.896 Multilign(20): 0.697 Positive Predictive Value ContextFold: 0.948 Multilign(20): 0.885 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	311 TurboFold(20) vs Multilign(20) Matthews Correlation Coefficient TurboFold(20): 0.889 Multilign(20): 0.784 Sensitivity TurboFold(20): 0.860 Multilign(20): 0.697 Positive Predictive Value TurboFold(20): 0.920 Multilign(20): 0.885 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	132 CentroidAlifold(seed) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.818 Multilign(20): 0.593 Sensitivity CentroidAlifold(seed): 0.744 Multilign(20): 0.447 Positive Predictive Value CentroidAlifold(seed): 0.901 Multilign(20): 0.793 Number of pairs reference - predicted secondary structure: 132 Wilcoxon single-rank test P-value: 3.56938820447e-08	311 CentroidHomfold‑LAST vs Multilign(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.857 Multilign(20): 0.784 Sensitivity CentroidHomfold‑LAST: 0.820 Multilign(20): 0.697 Positive Predictive Value CentroidHomfold‑LAST: 0.898 Multilign(20): 0.885 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	310 PETfold_pre2.0(seed) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.892 Multilign(20): 0.785 Sensitivity PETfold_pre2.0(seed): 0.841 Multilign(20): 0.697 Positive Predictive Value PETfold_pre2.0(seed): 0.947 Multilign(20): 0.887 Number of pairs reference - predicted secondary structure: 310 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 TurboFold(seed) vs Multilign(20) Matthews Correlation Coefficient TurboFold(seed): 0.877 Multilign(20): 0.574 Sensitivity TurboFold(seed): 0.871 Multilign(20): 0.422 Positive Predictive Value TurboFold(seed): 0.885 Multilign(20): 0.785 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 1.98760236454e-08	144 MXScarna(seed) vs Multilign(20) Matthews Correlation Coefficient MXScarna(seed): 0.792 Multilign(20): 0.623 Sensitivity MXScarna(seed): 0.757 Multilign(20): 0.481 Positive Predictive Value MXScarna(seed): 0.831 Multilign(20): 0.812 Number of pairs reference - predicted secondary structure: 144 Wilcoxon single-rank test P-value: 3.56938820447e-08	311 CentroidAlifold(20) vs Multilign(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.857 Multilign(20): 0.784 Sensitivity CentroidAlifold(20): 0.769 Multilign(20): 0.697 Positive Predictive Value CentroidAlifold(20): 0.957 Multilign(20): 0.885 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	311 PETfold_pre2.0(20) vs Multilign(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.858 Multilign(20): 0.784 Sensitivity PETfold_pre2.0(20): 0.756 Multilign(20): 0.697 Positive Predictive Value PETfold_pre2.0(20): 0.975 Multilign(20): 0.885 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	311 MXScarna(20) vs Multilign(20) Matthews Correlation Coefficient MXScarna(20): 0.841 Multilign(20): 0.784 Sensitivity MXScarna(20): 0.796 Multilign(20): 0.697 Positive Predictive Value MXScarna(20): 0.890 Multilign(20): 0.885 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	305 PPfold(20) vs Multilign(20) Matthews Correlation Coefficient PPfold(20): 0.850 Multilign(20): 0.789 Sensitivity PPfold(20): 0.741 Multilign(20): 0.704 Positive Predictive Value PPfold(20): 0.977 Multilign(20): 0.887 Number of pairs reference - predicted secondary structure: 305 Wilcoxon single-rank test P-value: 3.56938820447e-08	311 RNAalifold(20) vs Multilign(20) Matthews Correlation Coefficient RNAalifold(20): 0.824 Multilign(20): 0.784 Sensitivity RNAalifold(20): 0.705 Multilign(20): 0.697 Positive Predictive Value RNAalifold(20): 0.966 Multilign(20): 0.885 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	311 RSpredict(20) vs Multilign(20) Matthews Correlation Coefficient RSpredict(20): 0.793 Multilign(20): 0.784 Sensitivity RSpredict(20): 0.698 Multilign(20): 0.697 Positive Predictive Value RSpredict(20): 0.903 Multilign(20): 0.885 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 6.53888633552e-08	311 Multilign(20) vs IPknot Matthews Correlation Coefficient Multilign(20): 0.784 IPknot: 0.779 Sensitivity Multilign(20): 0.697 IPknot: 0.757 Positive Predictive Value Multilign(20): 0.885 IPknot: 0.804 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 2.28033735003e-07		+ Multilign(20) vs CentroidFold Matthews Correlation Coefficient Multilign(20): 0.784 CentroidFold: 0.735 Sensitivity Multilign(20): 0.697 CentroidFold: 0.709 Positive Predictive Value Multilign(20): 0.885 CentroidFold: 0.765 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Contrafold Matthews Correlation Coefficient Multilign(20): 0.784 Contrafold: 0.732 Sensitivity Multilign(20): 0.697 Contrafold: 0.728 Positive Predictive Value Multilign(20): 0.885 Contrafold: 0.740 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs RNASampler(20) Matthews Correlation Coefficient Multilign(20): 0.789 RNASampler(20): 0.781 Sensitivity Multilign(20): 0.703 RNASampler(20): 0.638 Positive Predictive Value Multilign(20): 0.888 RNASampler(20): 0.958 Number of pairs reference - predicted secondary structure: 306 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Murlet(20) Matthews Correlation Coefficient Multilign(20): 0.785 Murlet(20): 0.759 Sensitivity Multilign(20): 0.697 Murlet(20): 0.633 Positive Predictive Value Multilign(20): 0.887 Murlet(20): 0.912 Number of pairs reference - predicted secondary structure: 310 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CMfinder(seed) vs Multilign(20) Matthews Correlation Coefficient CMfinder(seed): 0.736 Multilign(20): 0.657 Sensitivity CMfinder(seed): 0.607 Multilign(20): 0.508 Positive Predictive Value CMfinder(seed): 0.898 Multilign(20): 0.856 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs MaxExpect Matthews Correlation Coefficient Multilign(20): 0.784 MaxExpect: 0.710 Sensitivity Multilign(20): 0.697 MaxExpect: 0.700 Positive Predictive Value Multilign(20): 0.885 MaxExpect: 0.725 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs CMfinder(20) Matthews Correlation Coefficient Multilign(20): 0.790 CMfinder(20): 0.742 Sensitivity Multilign(20): 0.706 CMfinder(20): 0.613 Positive Predictive Value Multilign(20): 0.887 CMfinder(20): 0.901 Number of pairs reference - predicted secondary structure: 307 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs CRWrnafold Matthews Correlation Coefficient Multilign(20): 0.784 CRWrnafold: 0.780 Sensitivity Multilign(20): 0.697 CRWrnafold: 0.767 Positive Predictive Value Multilign(20): 0.885 CRWrnafold: 0.795 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 0.000150377120024	+ Multilign(20) vs ProbKnot Matthews Correlation Coefficient Multilign(20): 0.784 ProbKnot: 0.706 Sensitivity Multilign(20): 0.697 ProbKnot: 0.701 Positive Predictive Value Multilign(20): 0.885 ProbKnot: 0.715 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Mastr(20) Matthews Correlation Coefficient Multilign(20): 0.784 Mastr(20): 0.712 Sensitivity Multilign(20): 0.697 Mastr(20): 0.644 Positive Predictive Value Multilign(20): 0.885 Mastr(20): 0.792 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Fold Matthews Correlation Coefficient Multilign(20): 0.784 Fold: 0.708 Sensitivity Multilign(20): 0.697 Fold: 0.706 Positive Predictive Value Multilign(20): 0.885 Fold: 0.714 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs UNAFold Matthews Correlation Coefficient Multilign(20): 0.784 UNAFold: 0.706 Sensitivity Multilign(20): 0.697 UNAFold: 0.695 Positive Predictive Value Multilign(20): 0.885 UNAFold: 0.721 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs PknotsRG Matthews Correlation Coefficient Multilign(20): 0.784 PknotsRG: 0.688 Sensitivity Multilign(20): 0.697 PknotsRG: 0.684 Positive Predictive Value Multilign(20): 0.885 PknotsRG: 0.696 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Sfold Matthews Correlation Coefficient Multilign(20): 0.784 Sfold: 0.696 Sensitivity Multilign(20): 0.697 Sfold: 0.660 Positive Predictive Value Multilign(20): 0.885 Sfold: 0.738 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNAalifold(seed) vs Multilign(20) Matthews Correlation Coefficient RNAalifold(seed): 0.612 Multilign(20): 0.583 Sensitivity RNAalifold(seed): 0.394 Multilign(20): 0.435 Positive Predictive Value RNAalifold(seed): 0.955 Multilign(20): 0.787 Number of pairs reference - predicted secondary structure: 128 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs RNAsubopt Matthews Correlation Coefficient Multilign(20): 0.784 RNAsubopt: 0.694 Sensitivity Multilign(20): 0.697 RNAsubopt: 0.693 Positive Predictive Value Multilign(20): 0.885 RNAsubopt: 0.699 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs HotKnots Matthews Correlation Coefficient Multilign(20): 0.784 HotKnots: 0.696 Sensitivity Multilign(20): 0.697 HotKnots: 0.692 Positive Predictive Value Multilign(20): 0.885 HotKnots: 0.703 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs RNAfold Matthews Correlation Coefficient Multilign(20): 0.784 RNAfold: 0.682 Sensitivity Multilign(20): 0.697 RNAfold: 0.678 Positive Predictive Value Multilign(20): 0.885 RNAfold: 0.691 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs RNAshapes Matthews Correlation Coefficient Multilign(20): 0.784 RNAshapes: 0.689 Sensitivity Multilign(20): 0.697 RNAshapes: 0.683 Positive Predictive Value Multilign(20): 0.885 RNAshapes: 0.699 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs RNASampler(seed) Matthews Correlation Coefficient Multilign(20): 0.692 RNASampler(seed): 0.571 Sensitivity Multilign(20): 0.552 RNASampler(seed): 0.343 Positive Predictive Value Multilign(20): 0.874 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Afold Matthews Correlation Coefficient Multilign(20): 0.728 Afold: 0.643 Sensitivity Multilign(20): 0.617 Afold: 0.631 Positive Predictive Value Multilign(20): 0.863 Afold: 0.659 Number of pairs reference - predicted secondary structure: 155 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Pknots Matthews Correlation Coefficient Multilign(20): 0.827 Pknots: 0.656 Sensitivity Multilign(20): 0.757 Pknots: 0.662 Positive Predictive Value Multilign(20): 0.906 Pknots: 0.654 Number of pairs reference - predicted secondary structure: 210 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs McQFold Matthews Correlation Coefficient Multilign(20): 0.784 McQFold: 0.614 Sensitivity Multilign(20): 0.697 McQFold: 0.591 Positive Predictive Value Multilign(20): 0.885 McQFold: 0.643 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Carnac(20) Matthews Correlation Coefficient Multilign(20): 0.784 Carnac(20): 0.683 Sensitivity Multilign(20): 0.697 Carnac(20): 0.511 Positive Predictive Value Multilign(20): 0.885 Carnac(20): 0.916 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs RNASLOpt Matthews Correlation Coefficient Multilign(20): 0.784 RNASLOpt: 0.640 Sensitivity Multilign(20): 0.697 RNASLOpt: 0.596 Positive Predictive Value Multilign(20): 0.885 RNASLOpt: 0.692 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Cylofold Matthews Correlation Coefficient Multilign(20): 0.783 Cylofold: 0.563 Sensitivity Multilign(20): 0.695 Cylofold: 0.549 Positive Predictive Value Multilign(20): 0.884 Cylofold: 0.583 Number of pairs reference - predicted secondary structure: 295 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Multilign(20) vs Multilign(seed) Matthews Correlation Coefficient Multilign(20): 0.588 Multilign(seed): 0.334 Sensitivity Multilign(20): 0.349 Multilign(seed): 0.186 Positive Predictive Value Multilign(20): 1.000 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ Multilign(20) vs RNAwolf Matthews Correlation Coefficient Multilign(20): 0.784 RNAwolf: 0.560 Sensitivity Multilign(20): 0.697 RNAwolf: 0.565 Positive Predictive Value Multilign(20): 0.885 RNAwolf: 0.560 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs PPfold(seed) Matthews Correlation Coefficient Multilign(20): 0.611 PPfold(seed): 0.354 Sensitivity Multilign(20): 0.462 PPfold(seed): 0.136 Positive Predictive Value Multilign(20): 0.811 PPfold(seed): 0.927 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Multilign(20) vs Murlet(seed) Matthews Correlation Coefficient Multilign(20): 0.673 Murlet(seed): 0.636 Sensitivity Multilign(20): 0.523 Murlet(seed): 0.428 Positive Predictive Value Multilign(20): 0.872 Murlet(seed): 0.952 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Alterna Matthews Correlation Coefficient Multilign(20): 0.829 Alterna: 0.616 Sensitivity Multilign(20): 0.758 Alterna: 0.624 Positive Predictive Value Multilign(20): 0.910 Alterna: 0.614 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Carnac(seed) Matthews Correlation Coefficient Multilign(20): 0.650 Carnac(seed): 0.442 Sensitivity Multilign(20): 0.513 Carnac(seed): 0.217 Positive Predictive Value Multilign(20): 0.829 Carnac(seed): 0.907 Number of pairs reference - predicted secondary structure: 66 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Vsfold4 Matthews Correlation Coefficient Multilign(20): 0.784 Vsfold4: 0.509 Sensitivity Multilign(20): 0.697 Vsfold4: 0.473 Positive Predictive Value Multilign(20): 0.885 Vsfold4: 0.555 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(20): 0.593 RSpredict(seed): 0.436 Sensitivity Multilign(20): 0.447 RSpredict(seed): 0.298 Positive Predictive Value Multilign(20): 0.793 RSpredict(seed): 0.645 Number of pairs reference - predicted secondary structure: 132 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Vsfold5 Matthews Correlation Coefficient Multilign(20): 0.784 Vsfold5: 0.469 Sensitivity Multilign(20): 0.697 Vsfold5: 0.449 Positive Predictive Value Multilign(20): 0.885 Vsfold5: 0.496 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs RDfolder Matthews Correlation Coefficient Multilign(20): 0.829 RDfolder: 0.561 Sensitivity Multilign(20): 0.758 RDfolder: 0.517 Positive Predictive Value Multilign(20): 0.910 RDfolder: 0.616 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs MCFold Matthews Correlation Coefficient Multilign(20): 0.774 MCFold: 0.498 Sensitivity Multilign(20): 0.681 MCFold: 0.558 Positive Predictive Value Multilign(20): 0.883 MCFold: 0.451 Number of pairs reference - predicted secondary structure: 251 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs NanoFolder Matthews Correlation Coefficient Multilign(20): 0.743 NanoFolder: 0.337 Sensitivity Multilign(20): 0.604 NanoFolder: 0.391 Positive Predictive Value Multilign(20): 0.918 NanoFolder: 0.298 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Multilign(20) vs Mastr(seed) Matthews Correlation Coefficient Multilign(20): 0.625 Mastr(seed): 0.276 Sensitivity Multilign(20): 0.483 Mastr(seed): 0.094 Positive Predictive Value Multilign(20): 0.814 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08
CentroidFold	882 ContextFold vs CentroidFold Matthews Correlation Coefficient ContextFold: 0.779 CentroidFold: 0.645 Sensitivity ContextFold: 0.741 CentroidFold: 0.612 Positive Predictive Value ContextFold: 0.823 CentroidFold: 0.684 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 TurboFold(20) vs CentroidFold Matthews Correlation Coefficient TurboFold(20): 0.889 CentroidFold: 0.735 Sensitivity TurboFold(20): 0.861 CentroidFold: 0.710 Positive Predictive Value TurboFold(20): 0.919 CentroidFold: 0.764 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	216 CentroidAlifold(seed) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.790 CentroidFold: 0.699 Sensitivity CentroidAlifold(seed): 0.699 CentroidFold: 0.665 Positive Predictive Value CentroidAlifold(seed): 0.896 CentroidFold: 0.739 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 CentroidHomfold‑LAST vs CentroidFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.736 CentroidFold: 0.645 Sensitivity CentroidHomfold‑LAST: 0.665 CentroidFold: 0.612 Positive Predictive Value CentroidHomfold‑LAST: 0.818 CentroidFold: 0.684 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	498 PETfold_pre2.0(seed) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.879 CentroidFold: 0.721 Sensitivity PETfold_pre2.0(seed): 0.825 CentroidFold: 0.691 Positive Predictive Value PETfold_pre2.0(seed): 0.938 CentroidFold: 0.755 Number of pairs reference - predicted secondary structure: 498 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 TurboFold(seed) vs CentroidFold Matthews Correlation Coefficient TurboFold(seed): 0.798 CentroidFold: 0.762 Sensitivity TurboFold(seed): 0.766 CentroidFold: 0.735 Positive Predictive Value TurboFold(seed): 0.835 CentroidFold: 0.794 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	233 MXScarna(seed) vs CentroidFold Matthews Correlation Coefficient MXScarna(seed): 0.750 CentroidFold: 0.699 Sensitivity MXScarna(seed): 0.712 CentroidFold: 0.665 Positive Predictive Value MXScarna(seed): 0.793 CentroidFold: 0.738 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 CentroidAlifold(20) vs CentroidFold Matthews Correlation Coefficient CentroidAlifold(20): 0.849 CentroidFold: 0.735 Sensitivity CentroidAlifold(20): 0.754 CentroidFold: 0.710 Positive Predictive Value CentroidAlifold(20): 0.957 CentroidFold: 0.764 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 PETfold_pre2.0(20) vs CentroidFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 CentroidFold: 0.735 Sensitivity PETfold_pre2.0(20): 0.737 CentroidFold: 0.710 Positive Predictive Value PETfold_pre2.0(20): 0.975 CentroidFold: 0.764 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 MXScarna(20) vs CentroidFold Matthews Correlation Coefficient MXScarna(20): 0.838 CentroidFold: 0.735 Sensitivity MXScarna(20): 0.791 CentroidFold: 0.710 Positive Predictive Value MXScarna(20): 0.891 CentroidFold: 0.764 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	314 PPfold(20) vs CentroidFold Matthews Correlation Coefficient PPfold(20): 0.839 CentroidFold: 0.733 Sensitivity PPfold(20): 0.721 CentroidFold: 0.707 Positive Predictive Value PPfold(20): 0.977 CentroidFold: 0.763 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RNAalifold(20) vs CentroidFold Matthews Correlation Coefficient RNAalifold(20): 0.816 CentroidFold: 0.735 Sensitivity RNAalifold(20): 0.690 CentroidFold: 0.710 Positive Predictive Value RNAalifold(20): 0.966 CentroidFold: 0.764 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RSpredict(20) vs CentroidFold Matthews Correlation Coefficient RSpredict(20): 0.789 CentroidFold: 0.735 Sensitivity RSpredict(20): 0.693 CentroidFold: 0.710 Positive Predictive Value RSpredict(20): 0.901 CentroidFold: 0.764 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 IPknot vs CentroidFold Matthews Correlation Coefficient IPknot: 0.694 CentroidFold: 0.645 Sensitivity IPknot: 0.661 CentroidFold: 0.612 Positive Predictive Value IPknot: 0.733 CentroidFold: 0.684 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	311 Multilign(20) vs CentroidFold Matthews Correlation Coefficient Multilign(20): 0.784 CentroidFold: 0.735 Sensitivity Multilign(20): 0.697 CentroidFold: 0.709 Positive Predictive Value Multilign(20): 0.885 CentroidFold: 0.765 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ CentroidFold vs Contrafold Matthews Correlation Coefficient CentroidFold: 0.645 Contrafold: 0.643 Sensitivity CentroidFold: 0.612 Contrafold: 0.634 Positive Predictive Value CentroidFold: 0.684 Contrafold: 0.657 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.85233844192e-08	- RNASampler(20) vs CentroidFold Matthews Correlation Coefficient RNASampler(20): 0.770 CentroidFold: 0.739 Sensitivity RNASampler(20): 0.622 CentroidFold: 0.712 Positive Predictive Value RNASampler(20): 0.957 CentroidFold: 0.769 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Murlet(20) vs CentroidFold Matthews Correlation Coefficient Murlet(20): 0.750 CentroidFold: 0.735 Sensitivity Murlet(20): 0.619 CentroidFold: 0.710 Positive Predictive Value Murlet(20): 0.913 CentroidFold: 0.765 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs CMfinder(seed) Matthews Correlation Coefficient CentroidFold: 0.599 CMfinder(seed): 0.571 Sensitivity CentroidFold: 0.514 CMfinder(seed): 0.439 Positive Predictive Value CentroidFold: 0.701 CMfinder(seed): 0.747 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ CentroidFold vs MaxExpect Matthews Correlation Coefficient CentroidFold: 0.645 MaxExpect: 0.633 Sensitivity CentroidFold: 0.612 MaxExpect: 0.617 Positive Predictive Value CentroidFold: 0.684 MaxExpect: 0.654 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	= CMfinder(20) vs CentroidFold Matthews Correlation Coefficient CMfinder(20): 0.735 CentroidFold: 0.734 Sensitivity CMfinder(20): 0.603 CentroidFold: 0.709 Positive Predictive Value CMfinder(20): 0.899 CentroidFold: 0.763 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 0.27038065226	+ CentroidFold vs CRWrnafold Matthews Correlation Coefficient CentroidFold: 0.645 CRWrnafold: 0.630 Sensitivity CentroidFold: 0.612 CRWrnafold: 0.618 Positive Predictive Value CentroidFold: 0.684 CRWrnafold: 0.648 Number of pairs reference - predicted secondary structure: 881 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs ProbKnot Matthews Correlation Coefficient CentroidFold: 0.645 ProbKnot: 0.630 Sensitivity CentroidFold: 0.612 ProbKnot: 0.622 Positive Predictive Value CentroidFold: 0.684 ProbKnot: 0.644 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Mastr(20) Matthews Correlation Coefficient CentroidFold: 0.735 Mastr(20): 0.708 Sensitivity CentroidFold: 0.710 Mastr(20): 0.635 Positive Predictive Value CentroidFold: 0.764 Mastr(20): 0.793 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ CentroidFold vs Fold Matthews Correlation Coefficient CentroidFold: 0.645 Fold: 0.628 Sensitivity CentroidFold: 0.612 Fold: 0.620 Positive Predictive Value CentroidFold: 0.684 Fold: 0.641 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs UNAFold Matthews Correlation Coefficient CentroidFold: 0.645 UNAFold: 0.620 Sensitivity CentroidFold: 0.612 UNAFold: 0.605 Positive Predictive Value CentroidFold: 0.684 UNAFold: 0.639 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs PknotsRG Matthews Correlation Coefficient CentroidFold: 0.645 PknotsRG: 0.617 Sensitivity CentroidFold: 0.612 PknotsRG: 0.610 Positive Predictive Value CentroidFold: 0.684 PknotsRG: 0.630 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Sfold Matthews Correlation Coefficient CentroidFold: 0.645 Sfold: 0.618 Sensitivity CentroidFold: 0.612 Sfold: 0.581 Positive Predictive Value CentroidFold: 0.684 Sfold: 0.663 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNAalifold(seed) Matthews Correlation Coefficient CentroidFold: 0.698 RNAalifold(seed): 0.610 Sensitivity CentroidFold: 0.663 RNAalifold(seed): 0.404 Positive Predictive Value CentroidFold: 0.738 RNAalifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNAsubopt Matthews Correlation Coefficient CentroidFold: 0.645 RNAsubopt: 0.615 Sensitivity CentroidFold: 0.612 RNAsubopt: 0.609 Positive Predictive Value CentroidFold: 0.684 RNAsubopt: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs HotKnots Matthews Correlation Coefficient CentroidFold: 0.645 HotKnots: 0.613 Sensitivity CentroidFold: 0.612 HotKnots: 0.607 Positive Predictive Value CentroidFold: 0.684 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 875 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNAfold Matthews Correlation Coefficient CentroidFold: 0.645 RNAfold: 0.612 Sensitivity CentroidFold: 0.612 RNAfold: 0.604 Positive Predictive Value CentroidFold: 0.684 RNAfold: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNAshapes Matthews Correlation Coefficient CentroidFold: 0.645 RNAshapes: 0.612 Sensitivity CentroidFold: 0.612 RNAshapes: 0.602 Positive Predictive Value CentroidFold: 0.684 RNAshapes: 0.628 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNASampler(seed) Matthews Correlation Coefficient CentroidFold: 0.614 RNASampler(seed): 0.557 Sensitivity CentroidFold: 0.530 RNASampler(seed): 0.389 Positive Predictive Value CentroidFold: 0.714 RNASampler(seed): 0.802 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Afold Matthews Correlation Coefficient CentroidFold: 0.609 Afold: 0.558 Sensitivity CentroidFold: 0.570 Afold: 0.541 Positive Predictive Value CentroidFold: 0.655 Afold: 0.582 Number of pairs reference - predicted secondary structure: 530 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Pknots Matthews Correlation Coefficient CentroidFold: 0.656 Pknots: 0.606 Sensitivity CentroidFold: 0.620 Pknots: 0.595 Positive Predictive Value CentroidFold: 0.701 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs McQFold Matthews Correlation Coefficient CentroidFold: 0.645 McQFold: 0.583 Sensitivity CentroidFold: 0.612 McQFold: 0.557 Positive Predictive Value CentroidFold: 0.684 McQFold: 0.616 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Carnac(20) Matthews Correlation Coefficient CentroidFold: 0.735 Carnac(20): 0.675 Sensitivity CentroidFold: 0.710 Carnac(20): 0.500 Positive Predictive Value CentroidFold: 0.764 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RNASLOpt Matthews Correlation Coefficient CentroidFold: 0.645 RNASLOpt: 0.562 Sensitivity CentroidFold: 0.612 RNASLOpt: 0.521 Positive Predictive Value CentroidFold: 0.684 RNASLOpt: 0.613 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Cylofold Matthews Correlation Coefficient CentroidFold: 0.676 Cylofold: 0.577 Sensitivity CentroidFold: 0.641 Cylofold: 0.554 Positive Predictive Value CentroidFold: 0.718 Cylofold: 0.608 Number of pairs reference - predicted secondary structure: 796 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Multilign(seed) Matthews Correlation Coefficient CentroidFold: 0.540 Multilign(seed): 0.485 Sensitivity CentroidFold: 0.456 Multilign(seed): 0.386 Positive Predictive Value CentroidFold: 0.649 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.86109605532e-08	+ CentroidFold vs RNAwolf Matthews Correlation Coefficient CentroidFold: 0.645 RNAwolf: 0.518 Sensitivity CentroidFold: 0.612 RNAwolf: 0.523 Positive Predictive Value CentroidFold: 0.684 RNAwolf: 0.520 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs PPfold(seed) Matthews Correlation Coefficient CentroidFold: 0.729 PPfold(seed): 0.380 Sensitivity CentroidFold: 0.696 PPfold(seed): 0.170 Positive Predictive Value CentroidFold: 0.767 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Murlet(seed) Matthews Correlation Coefficient CentroidFold: 0.638 Murlet(seed): 0.468 Sensitivity CentroidFold: 0.560 Murlet(seed): 0.266 Positive Predictive Value CentroidFold: 0.730 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Alterna Matthews Correlation Coefficient CentroidFold: 0.658 Alterna: 0.552 Sensitivity CentroidFold: 0.621 Alterna: 0.547 Positive Predictive Value CentroidFold: 0.703 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Carnac(seed) Matthews Correlation Coefficient CentroidFold: 0.674 Carnac(seed): 0.415 Sensitivity CentroidFold: 0.611 Carnac(seed): 0.196 Positive Predictive Value CentroidFold: 0.747 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Vsfold4 Matthews Correlation Coefficient CentroidFold: 0.645 Vsfold4: 0.487 Sensitivity CentroidFold: 0.612 Vsfold4: 0.447 Positive Predictive Value CentroidFold: 0.684 Vsfold4: 0.537 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RSpredict(seed) Matthews Correlation Coefficient CentroidFold: 0.699 RSpredict(seed): 0.373 Sensitivity CentroidFold: 0.665 RSpredict(seed): 0.251 Positive Predictive Value CentroidFold: 0.739 RSpredict(seed): 0.562 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Vsfold5 Matthews Correlation Coefficient CentroidFold: 0.645 Vsfold5: 0.477 Sensitivity CentroidFold: 0.612 Vsfold5: 0.450 Positive Predictive Value CentroidFold: 0.684 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs RDfolder Matthews Correlation Coefficient CentroidFold: 0.658 RDfolder: 0.520 Sensitivity CentroidFold: 0.621 RDfolder: 0.464 Positive Predictive Value CentroidFold: 0.703 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs MCFold Matthews Correlation Coefficient CentroidFold: 0.655 MCFold: 0.473 Sensitivity CentroidFold: 0.618 MCFold: 0.524 Positive Predictive Value CentroidFold: 0.699 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs NanoFolder Matthews Correlation Coefficient CentroidFold: 0.665 NanoFolder: 0.335 Sensitivity CentroidFold: 0.635 NanoFolder: 0.384 Positive Predictive Value CentroidFold: 0.701 NanoFolder: 0.301 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CentroidFold vs Mastr(seed) Matthews Correlation Coefficient CentroidFold: 0.699 Mastr(seed): 0.263 Sensitivity CentroidFold: 0.665 Mastr(seed): 0.089 Positive Predictive Value CentroidFold: 0.738 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08
Contrafold	882 ContextFold vs Contrafold Matthews Correlation Coefficient ContextFold: 0.779 Contrafold: 0.643 Sensitivity ContextFold: 0.741 Contrafold: 0.634 Positive Predictive Value ContextFold: 0.823 Contrafold: 0.657 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 TurboFold(20) vs Contrafold Matthews Correlation Coefficient TurboFold(20): 0.889 Contrafold: 0.733 Sensitivity TurboFold(20): 0.861 Contrafold: 0.729 Positive Predictive Value TurboFold(20): 0.919 Contrafold: 0.740 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	216 CentroidAlifold(seed) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.790 Contrafold: 0.692 Sensitivity CentroidAlifold(seed): 0.699 Contrafold: 0.681 Positive Predictive Value CentroidAlifold(seed): 0.896 Contrafold: 0.707 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 CentroidHomfold‑LAST vs Contrafold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.736 Contrafold: 0.643 Sensitivity CentroidHomfold‑LAST: 0.665 Contrafold: 0.634 Positive Predictive Value CentroidHomfold‑LAST: 0.818 Contrafold: 0.657 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	498 PETfold_pre2.0(seed) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.879 Contrafold: 0.715 Sensitivity PETfold_pre2.0(seed): 0.825 Contrafold: 0.710 Positive Predictive Value PETfold_pre2.0(seed): 0.938 Contrafold: 0.724 Number of pairs reference - predicted secondary structure: 498 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 TurboFold(seed) vs Contrafold Matthews Correlation Coefficient TurboFold(seed): 0.798 Contrafold: 0.757 Sensitivity TurboFold(seed): 0.766 Contrafold: 0.741 Positive Predictive Value TurboFold(seed): 0.835 Contrafold: 0.778 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	233 MXScarna(seed) vs Contrafold Matthews Correlation Coefficient MXScarna(seed): 0.750 Contrafold: 0.693 Sensitivity MXScarna(seed): 0.712 Contrafold: 0.682 Positive Predictive Value MXScarna(seed): 0.793 Contrafold: 0.707 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 CentroidAlifold(20) vs Contrafold Matthews Correlation Coefficient CentroidAlifold(20): 0.849 Contrafold: 0.733 Sensitivity CentroidAlifold(20): 0.754 Contrafold: 0.729 Positive Predictive Value CentroidAlifold(20): 0.957 Contrafold: 0.740 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 PETfold_pre2.0(20) vs Contrafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 Contrafold: 0.733 Sensitivity PETfold_pre2.0(20): 0.737 Contrafold: 0.729 Positive Predictive Value PETfold_pre2.0(20): 0.975 Contrafold: 0.740 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 MXScarna(20) vs Contrafold Matthews Correlation Coefficient MXScarna(20): 0.838 Contrafold: 0.733 Sensitivity MXScarna(20): 0.791 Contrafold: 0.729 Positive Predictive Value MXScarna(20): 0.891 Contrafold: 0.740 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	314 PPfold(20) vs Contrafold Matthews Correlation Coefficient PPfold(20): 0.839 Contrafold: 0.730 Sensitivity PPfold(20): 0.721 Contrafold: 0.726 Positive Predictive Value PPfold(20): 0.977 Contrafold: 0.738 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RNAalifold(20) vs Contrafold Matthews Correlation Coefficient RNAalifold(20): 0.816 Contrafold: 0.733 Sensitivity RNAalifold(20): 0.690 Contrafold: 0.729 Positive Predictive Value RNAalifold(20): 0.966 Contrafold: 0.740 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RSpredict(20) vs Contrafold Matthews Correlation Coefficient RSpredict(20): 0.789 Contrafold: 0.733 Sensitivity RSpredict(20): 0.693 Contrafold: 0.729 Positive Predictive Value RSpredict(20): 0.901 Contrafold: 0.740 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 IPknot vs Contrafold Matthews Correlation Coefficient IPknot: 0.694 Contrafold: 0.643 Sensitivity IPknot: 0.661 Contrafold: 0.634 Positive Predictive Value IPknot: 0.733 Contrafold: 0.657 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	311 Multilign(20) vs Contrafold Matthews Correlation Coefficient Multilign(20): 0.784 Contrafold: 0.732 Sensitivity Multilign(20): 0.697 Contrafold: 0.728 Positive Predictive Value Multilign(20): 0.885 Contrafold: 0.740 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 CentroidFold vs Contrafold Matthews Correlation Coefficient CentroidFold: 0.645 Contrafold: 0.643 Sensitivity CentroidFold: 0.612 Contrafold: 0.634 Positive Predictive Value CentroidFold: 0.684 Contrafold: 0.657 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.85233844192e-08		- RNASampler(20) vs Contrafold Matthews Correlation Coefficient RNASampler(20): 0.770 Contrafold: 0.736 Sensitivity RNASampler(20): 0.622 Contrafold: 0.731 Positive Predictive Value RNASampler(20): 0.957 Contrafold: 0.744 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Murlet(20) vs Contrafold Matthews Correlation Coefficient Murlet(20): 0.750 Contrafold: 0.733 Sensitivity Murlet(20): 0.619 Contrafold: 0.729 Positive Predictive Value Murlet(20): 0.913 Contrafold: 0.741 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs CMfinder(seed) Matthews Correlation Coefficient Contrafold: 0.594 CMfinder(seed): 0.571 Sensitivity Contrafold: 0.546 CMfinder(seed): 0.439 Positive Predictive Value Contrafold: 0.650 CMfinder(seed): 0.747 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 4.83792096436e-08	+ Contrafold vs MaxExpect Matthews Correlation Coefficient Contrafold: 0.643 MaxExpect: 0.633 Sensitivity Contrafold: 0.634 MaxExpect: 0.617 Positive Predictive Value Contrafold: 0.657 MaxExpect: 0.654 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	= CMfinder(20) vs Contrafold Matthews Correlation Coefficient CMfinder(20): 0.735 Contrafold: 0.732 Sensitivity CMfinder(20): 0.603 Contrafold: 0.728 Positive Predictive Value CMfinder(20): 0.899 Contrafold: 0.739 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 0.0124164808574	+ Contrafold vs CRWrnafold Matthews Correlation Coefficient Contrafold: 0.643 CRWrnafold: 0.630 Sensitivity Contrafold: 0.634 CRWrnafold: 0.618 Positive Predictive Value Contrafold: 0.657 CRWrnafold: 0.648 Number of pairs reference - predicted secondary structure: 881 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ Contrafold vs ProbKnot Matthews Correlation Coefficient Contrafold: 0.643 ProbKnot: 0.630 Sensitivity Contrafold: 0.634 ProbKnot: 0.622 Positive Predictive Value Contrafold: 0.657 ProbKnot: 0.644 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Mastr(20) Matthews Correlation Coefficient Contrafold: 0.733 Mastr(20): 0.708 Sensitivity Contrafold: 0.729 Mastr(20): 0.635 Positive Predictive Value Contrafold: 0.740 Mastr(20): 0.793 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Fold Matthews Correlation Coefficient Contrafold: 0.643 Fold: 0.628 Sensitivity Contrafold: 0.634 Fold: 0.620 Positive Predictive Value Contrafold: 0.657 Fold: 0.641 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs UNAFold Matthews Correlation Coefficient Contrafold: 0.643 UNAFold: 0.620 Sensitivity Contrafold: 0.634 UNAFold: 0.605 Positive Predictive Value Contrafold: 0.657 UNAFold: 0.639 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs PknotsRG Matthews Correlation Coefficient Contrafold: 0.643 PknotsRG: 0.617 Sensitivity Contrafold: 0.634 PknotsRG: 0.610 Positive Predictive Value Contrafold: 0.657 PknotsRG: 0.630 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Sfold Matthews Correlation Coefficient Contrafold: 0.643 Sfold: 0.618 Sensitivity Contrafold: 0.634 Sfold: 0.581 Positive Predictive Value Contrafold: 0.657 Sfold: 0.663 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNAalifold(seed) Matthews Correlation Coefficient Contrafold: 0.693 RNAalifold(seed): 0.610 Sensitivity Contrafold: 0.681 RNAalifold(seed): 0.404 Positive Predictive Value Contrafold: 0.709 RNAalifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNAsubopt Matthews Correlation Coefficient Contrafold: 0.643 RNAsubopt: 0.615 Sensitivity Contrafold: 0.634 RNAsubopt: 0.609 Positive Predictive Value Contrafold: 0.657 RNAsubopt: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs HotKnots Matthews Correlation Coefficient Contrafold: 0.643 HotKnots: 0.613 Sensitivity Contrafold: 0.635 HotKnots: 0.607 Positive Predictive Value Contrafold: 0.657 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 875 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNAfold Matthews Correlation Coefficient Contrafold: 0.643 RNAfold: 0.612 Sensitivity Contrafold: 0.634 RNAfold: 0.604 Positive Predictive Value Contrafold: 0.657 RNAfold: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNAshapes Matthews Correlation Coefficient Contrafold: 0.643 RNAshapes: 0.612 Sensitivity Contrafold: 0.634 RNAshapes: 0.602 Positive Predictive Value Contrafold: 0.657 RNAshapes: 0.628 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNASampler(seed) Matthews Correlation Coefficient Contrafold: 0.609 RNASampler(seed): 0.557 Sensitivity Contrafold: 0.561 RNASampler(seed): 0.389 Positive Predictive Value Contrafold: 0.665 RNASampler(seed): 0.802 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Afold Matthews Correlation Coefficient Contrafold: 0.609 Afold: 0.558 Sensitivity Contrafold: 0.592 Afold: 0.541 Positive Predictive Value Contrafold: 0.631 Afold: 0.582 Number of pairs reference - predicted secondary structure: 530 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Pknots Matthews Correlation Coefficient Contrafold: 0.656 Pknots: 0.606 Sensitivity Contrafold: 0.645 Pknots: 0.595 Positive Predictive Value Contrafold: 0.673 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs McQFold Matthews Correlation Coefficient Contrafold: 0.643 McQFold: 0.583 Sensitivity Contrafold: 0.634 McQFold: 0.557 Positive Predictive Value Contrafold: 0.657 McQFold: 0.616 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Carnac(20) Matthews Correlation Coefficient Contrafold: 0.733 Carnac(20): 0.675 Sensitivity Contrafold: 0.729 Carnac(20): 0.500 Positive Predictive Value Contrafold: 0.740 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RNASLOpt Matthews Correlation Coefficient Contrafold: 0.643 RNASLOpt: 0.562 Sensitivity Contrafold: 0.634 RNASLOpt: 0.521 Positive Predictive Value Contrafold: 0.657 RNASLOpt: 0.613 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Cylofold Matthews Correlation Coefficient Contrafold: 0.673 Cylofold: 0.577 Sensitivity Contrafold: 0.662 Cylofold: 0.554 Positive Predictive Value Contrafold: 0.689 Cylofold: 0.608 Number of pairs reference - predicted secondary structure: 796 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Multilign(seed) Matthews Correlation Coefficient Contrafold: 0.525 Multilign(seed): 0.485 Sensitivity Contrafold: 0.460 Multilign(seed): 0.386 Positive Predictive Value Contrafold: 0.607 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.89649746203e-08	+ Contrafold vs RNAwolf Matthews Correlation Coefficient Contrafold: 0.643 RNAwolf: 0.518 Sensitivity Contrafold: 0.634 RNAwolf: 0.523 Positive Predictive Value Contrafold: 0.657 RNAwolf: 0.520 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs PPfold(seed) Matthews Correlation Coefficient Contrafold: 0.722 PPfold(seed): 0.380 Sensitivity Contrafold: 0.706 PPfold(seed): 0.170 Positive Predictive Value Contrafold: 0.743 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Murlet(seed) Matthews Correlation Coefficient Contrafold: 0.633 Murlet(seed): 0.468 Sensitivity Contrafold: 0.589 Murlet(seed): 0.266 Positive Predictive Value Contrafold: 0.684 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Alterna Matthews Correlation Coefficient Contrafold: 0.657 Alterna: 0.552 Sensitivity Contrafold: 0.646 Alterna: 0.547 Positive Predictive Value Contrafold: 0.675 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Carnac(seed) Matthews Correlation Coefficient Contrafold: 0.665 Carnac(seed): 0.415 Sensitivity Contrafold: 0.633 Carnac(seed): 0.196 Positive Predictive Value Contrafold: 0.702 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Vsfold4 Matthews Correlation Coefficient Contrafold: 0.643 Vsfold4: 0.487 Sensitivity Contrafold: 0.634 Vsfold4: 0.447 Positive Predictive Value Contrafold: 0.657 Vsfold4: 0.537 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RSpredict(seed) Matthews Correlation Coefficient Contrafold: 0.692 RSpredict(seed): 0.373 Sensitivity Contrafold: 0.681 RSpredict(seed): 0.251 Positive Predictive Value Contrafold: 0.707 RSpredict(seed): 0.562 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Vsfold5 Matthews Correlation Coefficient Contrafold: 0.643 Vsfold5: 0.477 Sensitivity Contrafold: 0.634 Vsfold5: 0.450 Positive Predictive Value Contrafold: 0.657 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs RDfolder Matthews Correlation Coefficient Contrafold: 0.657 RDfolder: 0.520 Sensitivity Contrafold: 0.646 RDfolder: 0.464 Positive Predictive Value Contrafold: 0.675 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs MCFold Matthews Correlation Coefficient Contrafold: 0.654 MCFold: 0.473 Sensitivity Contrafold: 0.642 MCFold: 0.524 Positive Predictive Value Contrafold: 0.672 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs NanoFolder Matthews Correlation Coefficient Contrafold: 0.668 NanoFolder: 0.335 Sensitivity Contrafold: 0.658 NanoFolder: 0.384 Positive Predictive Value Contrafold: 0.683 NanoFolder: 0.301 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Contrafold vs Mastr(seed) Matthews Correlation Coefficient Contrafold: 0.693 Mastr(seed): 0.263 Sensitivity Contrafold: 0.682 Mastr(seed): 0.089 Positive Predictive Value Contrafold: 0.707 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNASampler(20)	315 ContextFold vs RNASampler(20) Matthews Correlation Coefficient ContextFold: 0.924 RNASampler(20): 0.770 Sensitivity ContextFold: 0.898 RNASampler(20): 0.622 Positive Predictive Value ContextFold: 0.951 RNASampler(20): 0.957 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	315 TurboFold(20) vs RNASampler(20) Matthews Correlation Coefficient TurboFold(20): 0.891 RNASampler(20): 0.770 Sensitivity TurboFold(20): 0.863 RNASampler(20): 0.622 Positive Predictive Value TurboFold(20): 0.921 RNASampler(20): 0.957 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	137 CentroidAlifold(seed) vs RNASampler(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.819 RNASampler(20): 0.604 Sensitivity CentroidAlifold(seed): 0.744 RNASampler(20): 0.394 Positive Predictive Value CentroidAlifold(seed): 0.904 RNASampler(20): 0.931 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 3.56938820447e-08	315 CentroidHomfold‑LAST vs RNASampler(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.859 RNASampler(20): 0.770 Sensitivity CentroidHomfold‑LAST: 0.821 RNASampler(20): 0.622 Positive Predictive Value CentroidHomfold‑LAST: 0.900 RNASampler(20): 0.957 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	314 PETfold_pre2.0(seed) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.888 RNASampler(20): 0.771 Sensitivity PETfold_pre2.0(seed): 0.834 RNASampler(20): 0.623 Positive Predictive Value PETfold_pre2.0(seed): 0.946 RNASampler(20): 0.957 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 TurboFold(seed) vs RNASampler(20) Matthews Correlation Coefficient TurboFold(seed): 0.880 RNASampler(20): 0.616 Sensitivity TurboFold(seed): 0.875 RNASampler(20): 0.402 Positive Predictive Value TurboFold(seed): 0.886 RNASampler(20): 0.948 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.1413769576e-08	149 MXScarna(seed) vs RNASampler(20) Matthews Correlation Coefficient MXScarna(seed): 0.798 RNASampler(20): 0.632 Sensitivity MXScarna(seed): 0.761 RNASampler(20): 0.427 Positive Predictive Value MXScarna(seed): 0.839 RNASampler(20): 0.939 Number of pairs reference - predicted secondary structure: 149 Wilcoxon single-rank test P-value: 3.56938820447e-08	315 CentroidAlifold(20) vs RNASampler(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.852 RNASampler(20): 0.770 Sensitivity CentroidAlifold(20): 0.759 RNASampler(20): 0.622 Positive Predictive Value CentroidAlifold(20): 0.957 RNASampler(20): 0.957 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	315 PETfold_pre2.0(20) vs RNASampler(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.850 RNASampler(20): 0.770 Sensitivity PETfold_pre2.0(20): 0.743 RNASampler(20): 0.622 Positive Predictive Value PETfold_pre2.0(20): 0.975 RNASampler(20): 0.957 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	315 MXScarna(20) vs RNASampler(20) Matthews Correlation Coefficient MXScarna(20): 0.841 RNASampler(20): 0.770 Sensitivity MXScarna(20): 0.796 RNASampler(20): 0.622 Positive Predictive Value MXScarna(20): 0.890 RNASampler(20): 0.957 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	310 PPfold(20) vs RNASampler(20) Matthews Correlation Coefficient PPfold(20): 0.841 RNASampler(20): 0.774 Sensitivity PPfold(20): 0.725 RNASampler(20): 0.629 Positive Predictive Value PPfold(20): 0.977 RNASampler(20): 0.956 Number of pairs reference - predicted secondary structure: 310 Wilcoxon single-rank test P-value: 3.56938820447e-08	315 RNAalifold(20) vs RNASampler(20) Matthews Correlation Coefficient RNAalifold(20): 0.819 RNASampler(20): 0.770 Sensitivity RNAalifold(20): 0.695 RNASampler(20): 0.622 Positive Predictive Value RNAalifold(20): 0.966 RNASampler(20): 0.957 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	315 RSpredict(20) vs RNASampler(20) Matthews Correlation Coefficient RSpredict(20): 0.793 RNASampler(20): 0.770 Sensitivity RSpredict(20): 0.700 RNASampler(20): 0.622 Positive Predictive Value RSpredict(20): 0.902 RNASampler(20): 0.957 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	315 IPknot vs RNASampler(20) Matthews Correlation Coefficient IPknot: 0.785 RNASampler(20): 0.770 Sensitivity IPknot: 0.763 RNASampler(20): 0.622 Positive Predictive Value IPknot: 0.810 RNASampler(20): 0.957 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	306 Multilign(20) vs RNASampler(20) Matthews Correlation Coefficient Multilign(20): 0.789 RNASampler(20): 0.781 Sensitivity Multilign(20): 0.703 RNASampler(20): 0.638 Positive Predictive Value Multilign(20): 0.888 RNASampler(20): 0.958 Number of pairs reference - predicted secondary structure: 306 Wilcoxon single-rank test P-value: 3.56938820447e-08	315 RNASampler(20) vs CentroidFold Matthews Correlation Coefficient RNASampler(20): 0.770 CentroidFold: 0.739 Sensitivity RNASampler(20): 0.622 CentroidFold: 0.712 Positive Predictive Value RNASampler(20): 0.957 CentroidFold: 0.769 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	315 RNASampler(20) vs Contrafold Matthews Correlation Coefficient RNASampler(20): 0.770 Contrafold: 0.736 Sensitivity RNASampler(20): 0.622 Contrafold: 0.731 Positive Predictive Value RNASampler(20): 0.957 Contrafold: 0.744 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ RNASampler(20) vs Murlet(20) Matthews Correlation Coefficient RNASampler(20): 0.771 Murlet(20): 0.753 Sensitivity RNASampler(20): 0.623 Murlet(20): 0.624 Positive Predictive Value RNASampler(20): 0.957 Murlet(20): 0.913 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CMfinder(seed) vs RNASampler(20) Matthews Correlation Coefficient CMfinder(seed): 0.736 RNASampler(20): 0.593 Sensitivity CMfinder(seed): 0.607 RNASampler(20): 0.399 Positive Predictive Value CMfinder(seed): 0.898 RNASampler(20): 0.888 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNASampler(20) vs MaxExpect Matthews Correlation Coefficient RNASampler(20): 0.770 MaxExpect: 0.714 Sensitivity RNASampler(20): 0.622 MaxExpect: 0.703 Positive Predictive Value RNASampler(20): 0.957 MaxExpect: 0.728 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs CMfinder(20) Matthews Correlation Coefficient RNASampler(20): 0.775 CMfinder(20): 0.736 Sensitivity RNASampler(20): 0.629 CMfinder(20): 0.605 Positive Predictive Value RNASampler(20): 0.957 CMfinder(20): 0.898 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CRWrnafold vs RNASampler(20) Matthews Correlation Coefficient CRWrnafold: 0.784 RNASampler(20): 0.770 Sensitivity CRWrnafold: 0.771 RNASampler(20): 0.622 Positive Predictive Value CRWrnafold: 0.799 RNASampler(20): 0.957 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ RNASampler(20) vs ProbKnot Matthews Correlation Coefficient RNASampler(20): 0.770 ProbKnot: 0.709 Sensitivity RNASampler(20): 0.622 ProbKnot: 0.704 Positive Predictive Value RNASampler(20): 0.957 ProbKnot: 0.718 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Mastr(20) Matthews Correlation Coefficient RNASampler(20): 0.770 Mastr(20): 0.710 Sensitivity RNASampler(20): 0.622 Mastr(20): 0.639 Positive Predictive Value RNASampler(20): 0.957 Mastr(20): 0.793 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Fold Matthews Correlation Coefficient RNASampler(20): 0.770 Fold: 0.713 Sensitivity RNASampler(20): 0.622 Fold: 0.711 Positive Predictive Value RNASampler(20): 0.957 Fold: 0.718 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs UNAFold Matthews Correlation Coefficient RNASampler(20): 0.770 UNAFold: 0.708 Sensitivity RNASampler(20): 0.622 UNAFold: 0.696 Positive Predictive Value RNASampler(20): 0.957 UNAFold: 0.723 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs PknotsRG Matthews Correlation Coefficient RNASampler(20): 0.770 PknotsRG: 0.691 Sensitivity RNASampler(20): 0.622 PknotsRG: 0.687 Positive Predictive Value RNASampler(20): 0.957 PknotsRG: 0.699 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Sfold Matthews Correlation Coefficient RNASampler(20): 0.770 Sfold: 0.700 Sensitivity RNASampler(20): 0.622 Sfold: 0.664 Positive Predictive Value RNASampler(20): 0.957 Sfold: 0.743 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNAalifold(seed) vs RNASampler(20) Matthews Correlation Coefficient RNAalifold(seed): 0.605 RNASampler(20): 0.591 Sensitivity RNAalifold(seed): 0.385 RNASampler(20): 0.378 Positive Predictive Value RNAalifold(seed): 0.954 RNASampler(20): 0.928 Number of pairs reference - predicted secondary structure: 133 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs RNAsubopt Matthews Correlation Coefficient RNASampler(20): 0.770 RNAsubopt: 0.697 Sensitivity RNASampler(20): 0.622 RNAsubopt: 0.695 Positive Predictive Value RNASampler(20): 0.957 RNAsubopt: 0.703 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs HotKnots Matthews Correlation Coefficient RNASampler(20): 0.770 HotKnots: 0.698 Sensitivity RNASampler(20): 0.622 HotKnots: 0.694 Positive Predictive Value RNASampler(20): 0.957 HotKnots: 0.706 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs RNAfold Matthews Correlation Coefficient RNASampler(20): 0.770 RNAfold: 0.685 Sensitivity RNASampler(20): 0.622 RNAfold: 0.680 Positive Predictive Value RNASampler(20): 0.957 RNAfold: 0.695 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs RNAshapes Matthews Correlation Coefficient RNASampler(20): 0.770 RNAshapes: 0.695 Sensitivity RNASampler(20): 0.622 RNAshapes: 0.690 Positive Predictive Value RNASampler(20): 0.957 RNAshapes: 0.705 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs RNASampler(seed) Matthews Correlation Coefficient RNASampler(20): 0.640 RNASampler(seed): 0.571 Sensitivity RNASampler(20): 0.454 RNASampler(seed): 0.343 Positive Predictive Value RNASampler(20): 0.909 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ RNASampler(20) vs Afold Matthews Correlation Coefficient RNASampler(20): 0.683 Afold: 0.649 Sensitivity RNASampler(20): 0.500 Afold: 0.636 Positive Predictive Value RNASampler(20): 0.937 Afold: 0.667 Number of pairs reference - predicted secondary structure: 158 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Pknots Matthews Correlation Coefficient RNASampler(20): 0.857 Pknots: 0.660 Sensitivity RNASampler(20): 0.758 Pknots: 0.666 Positive Predictive Value RNASampler(20): 0.971 Pknots: 0.658 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs McQFold Matthews Correlation Coefficient RNASampler(20): 0.770 McQFold: 0.613 Sensitivity RNASampler(20): 0.622 McQFold: 0.589 Positive Predictive Value RNASampler(20): 0.957 McQFold: 0.643 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Carnac(20) Matthews Correlation Coefficient RNASampler(20): 0.770 Carnac(20): 0.678 Sensitivity RNASampler(20): 0.622 Carnac(20): 0.504 Positive Predictive Value RNASampler(20): 0.957 Carnac(20): 0.916 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs RNASLOpt Matthews Correlation Coefficient RNASampler(20): 0.770 RNASLOpt: 0.641 Sensitivity RNASampler(20): 0.622 RNASLOpt: 0.596 Positive Predictive Value RNASampler(20): 0.957 RNASLOpt: 0.693 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Cylofold Matthews Correlation Coefficient RNASampler(20): 0.773 Cylofold: 0.559 Sensitivity RNASampler(20): 0.625 Cylofold: 0.546 Positive Predictive Value RNASampler(20): 0.959 Cylofold: 0.579 Number of pairs reference - predicted secondary structure: 299 Wilcoxon single-rank test P-value: 3.56938820447e-08	? RNASampler(20) vs Multilign(seed) Matthews Correlation Coefficient RNASampler(20): 0.536 Multilign(seed): 0.334 Sensitivity RNASampler(20): 0.349 Multilign(seed): 0.186 Positive Predictive Value RNASampler(20): 0.833 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ RNASampler(20) vs RNAwolf Matthews Correlation Coefficient RNASampler(20): 0.770 RNAwolf: 0.560 Sensitivity RNASampler(20): 0.622 RNAwolf: 0.565 Positive Predictive Value RNASampler(20): 0.957 RNAwolf: 0.561 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs PPfold(seed) Matthews Correlation Coefficient RNASampler(20): 0.589 PPfold(seed): 0.344 Sensitivity RNASampler(20): 0.363 PPfold(seed): 0.128 Positive Predictive Value RNASampler(20): 0.960 PPfold(seed): 0.927 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	- Murlet(seed) vs RNASampler(20) Matthews Correlation Coefficient Murlet(seed): 0.636 RNASampler(20): 0.621 Sensitivity Murlet(seed): 0.428 RNASampler(20): 0.426 Positive Predictive Value Murlet(seed): 0.952 RNASampler(20): 0.912 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 2.63254822069e-07	+ RNASampler(20) vs Alterna Matthews Correlation Coefficient RNASampler(20): 0.859 Alterna: 0.620 Sensitivity RNASampler(20): 0.761 Alterna: 0.627 Positive Predictive Value RNASampler(20): 0.971 Alterna: 0.618 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(20): 0.639 Carnac(seed): 0.431 Sensitivity RNASampler(20): 0.434 Carnac(seed): 0.206 Positive Predictive Value RNASampler(20): 0.946 Carnac(seed): 0.907 Number of pairs reference - predicted secondary structure: 68 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Vsfold4 Matthews Correlation Coefficient RNASampler(20): 0.770 Vsfold4: 0.505 Sensitivity RNASampler(20): 0.622 Vsfold4: 0.469 Positive Predictive Value RNASampler(20): 0.957 Vsfold4: 0.549 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(20): 0.604 RSpredict(seed): 0.417 Sensitivity RNASampler(20): 0.394 RSpredict(seed): 0.282 Positive Predictive Value RNASampler(20): 0.931 RSpredict(seed): 0.626 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Vsfold5 Matthews Correlation Coefficient RNASampler(20): 0.770 Vsfold5: 0.462 Sensitivity RNASampler(20): 0.622 Vsfold5: 0.442 Positive Predictive Value RNASampler(20): 0.957 Vsfold5: 0.489 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs RDfolder Matthews Correlation Coefficient RNASampler(20): 0.859 RDfolder: 0.560 Sensitivity RNASampler(20): 0.761 RDfolder: 0.516 Positive Predictive Value RNASampler(20): 0.971 RDfolder: 0.614 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs MCFold Matthews Correlation Coefficient RNASampler(20): 0.771 MCFold: 0.500 Sensitivity RNASampler(20): 0.623 MCFold: 0.560 Positive Predictive Value RNASampler(20): 0.956 MCFold: 0.454 Number of pairs reference - predicted secondary structure: 254 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs NanoFolder Matthews Correlation Coefficient RNASampler(20): 0.732 NanoFolder: 0.338 Sensitivity RNASampler(20): 0.555 NanoFolder: 0.392 Positive Predictive Value RNASampler(20): 0.968 NanoFolder: 0.300 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(20) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(20): 0.634 Mastr(seed): 0.269 Sensitivity RNASampler(20): 0.430 Mastr(seed): 0.089 Positive Predictive Value RNASampler(20): 0.940 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 150 Wilcoxon single-rank test P-value: 3.56938820447e-08
Murlet(20)	319 ContextFold vs Murlet(20) Matthews Correlation Coefficient ContextFold: 0.923 Murlet(20): 0.750 Sensitivity ContextFold: 0.898 Murlet(20): 0.619 Positive Predictive Value ContextFold: 0.950 Murlet(20): 0.913 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	319 TurboFold(20) vs Murlet(20) Matthews Correlation Coefficient TurboFold(20): 0.890 Murlet(20): 0.750 Sensitivity TurboFold(20): 0.862 Murlet(20): 0.619 Positive Predictive Value TurboFold(20): 0.920 Murlet(20): 0.913 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	140 CentroidAlifold(seed) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.816 Murlet(20): 0.609 Sensitivity CentroidAlifold(seed): 0.744 Murlet(20): 0.404 Positive Predictive Value CentroidAlifold(seed): 0.898 Murlet(20): 0.922 Number of pairs reference - predicted secondary structure: 140 Wilcoxon single-rank test P-value: 3.56938820447e-08	319 CentroidHomfold‑LAST vs Murlet(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.859 Murlet(20): 0.750 Sensitivity CentroidHomfold‑LAST: 0.821 Murlet(20): 0.619 Positive Predictive Value CentroidHomfold‑LAST: 0.901 Murlet(20): 0.913 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	319 PETfold_pre2.0(seed) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.885 Murlet(20): 0.750 Sensitivity PETfold_pre2.0(seed): 0.832 Murlet(20): 0.619 Positive Predictive Value PETfold_pre2.0(seed): 0.944 Murlet(20): 0.913 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 TurboFold(seed) vs Murlet(20) Matthews Correlation Coefficient TurboFold(seed): 0.902 Murlet(20): 0.628 Sensitivity TurboFold(seed): 0.892 Murlet(20): 0.414 Positive Predictive Value TurboFold(seed): 0.914 Murlet(20): 0.957 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 2.89169006118e-08	152 MXScarna(seed) vs Murlet(20) Matthews Correlation Coefficient MXScarna(seed): 0.793 Murlet(20): 0.625 Sensitivity MXScarna(seed): 0.756 Murlet(20): 0.428 Positive Predictive Value MXScarna(seed): 0.834 Murlet(20): 0.918 Number of pairs reference - predicted secondary structure: 152 Wilcoxon single-rank test P-value: 3.56938820447e-08	319 CentroidAlifold(20) vs Murlet(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.849 Murlet(20): 0.750 Sensitivity CentroidAlifold(20): 0.754 Murlet(20): 0.619 Positive Predictive Value CentroidAlifold(20): 0.958 Murlet(20): 0.913 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	319 PETfold_pre2.0(20) vs Murlet(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.848 Murlet(20): 0.750 Sensitivity PETfold_pre2.0(20): 0.739 Murlet(20): 0.619 Positive Predictive Value PETfold_pre2.0(20): 0.976 Murlet(20): 0.913 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	319 MXScarna(20) vs Murlet(20) Matthews Correlation Coefficient MXScarna(20): 0.839 Murlet(20): 0.750 Sensitivity MXScarna(20): 0.791 Murlet(20): 0.619 Positive Predictive Value MXScarna(20): 0.892 Murlet(20): 0.913 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	313 PPfold(20) vs Murlet(20) Matthews Correlation Coefficient PPfold(20): 0.840 Murlet(20): 0.754 Sensitivity PPfold(20): 0.723 Murlet(20): 0.625 Positive Predictive Value PPfold(20): 0.977 Murlet(20): 0.912 Number of pairs reference - predicted secondary structure: 313 Wilcoxon single-rank test P-value: 3.56938820447e-08	319 RNAalifold(20) vs Murlet(20) Matthews Correlation Coefficient RNAalifold(20): 0.816 Murlet(20): 0.750 Sensitivity RNAalifold(20): 0.690 Murlet(20): 0.619 Positive Predictive Value RNAalifold(20): 0.968 Murlet(20): 0.913 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	319 RSpredict(20) vs Murlet(20) Matthews Correlation Coefficient RSpredict(20): 0.789 Murlet(20): 0.750 Sensitivity RSpredict(20): 0.693 Murlet(20): 0.619 Positive Predictive Value RSpredict(20): 0.901 Murlet(20): 0.913 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	319 IPknot vs Murlet(20) Matthews Correlation Coefficient IPknot: 0.783 Murlet(20): 0.750 Sensitivity IPknot: 0.762 Murlet(20): 0.619 Positive Predictive Value IPknot: 0.808 Murlet(20): 0.913 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	310 Multilign(20) vs Murlet(20) Matthews Correlation Coefficient Multilign(20): 0.785 Murlet(20): 0.759 Sensitivity Multilign(20): 0.697 Murlet(20): 0.633 Positive Predictive Value Multilign(20): 0.887 Murlet(20): 0.912 Number of pairs reference - predicted secondary structure: 310 Wilcoxon single-rank test P-value: 3.56938820447e-08	319 Murlet(20) vs CentroidFold Matthews Correlation Coefficient Murlet(20): 0.750 CentroidFold: 0.735 Sensitivity Murlet(20): 0.619 CentroidFold: 0.710 Positive Predictive Value Murlet(20): 0.913 CentroidFold: 0.765 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	319 Murlet(20) vs Contrafold Matthews Correlation Coefficient Murlet(20): 0.750 Contrafold: 0.733 Sensitivity Murlet(20): 0.619 Contrafold: 0.729 Positive Predictive Value Murlet(20): 0.913 Contrafold: 0.741 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	314 RNASampler(20) vs Murlet(20) Matthews Correlation Coefficient RNASampler(20): 0.771 Murlet(20): 0.753 Sensitivity RNASampler(20): 0.623 Murlet(20): 0.624 Positive Predictive Value RNASampler(20): 0.957 Murlet(20): 0.913 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08		- CMfinder(seed) vs Murlet(20) Matthews Correlation Coefficient CMfinder(seed): 0.736 Murlet(20): 0.649 Sensitivity CMfinder(seed): 0.607 Murlet(20): 0.483 Positive Predictive Value CMfinder(seed): 0.898 Murlet(20): 0.878 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.23657817852e-08	+ Murlet(20) vs MaxExpect Matthews Correlation Coefficient Murlet(20): 0.750 MaxExpect: 0.712 Sensitivity Murlet(20): 0.619 MaxExpect: 0.702 Positive Predictive Value Murlet(20): 0.913 MaxExpect: 0.726 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs CMfinder(20) Matthews Correlation Coefficient Murlet(20): 0.754 CMfinder(20): 0.735 Sensitivity Murlet(20): 0.626 CMfinder(20): 0.603 Positive Predictive Value Murlet(20): 0.913 CMfinder(20): 0.899 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	- CRWrnafold vs Murlet(20) Matthews Correlation Coefficient CRWrnafold: 0.783 Murlet(20): 0.750 Sensitivity CRWrnafold: 0.771 Murlet(20): 0.619 Positive Predictive Value CRWrnafold: 0.798 Murlet(20): 0.913 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs ProbKnot Matthews Correlation Coefficient Murlet(20): 0.750 ProbKnot: 0.707 Sensitivity Murlet(20): 0.619 ProbKnot: 0.703 Positive Predictive Value Murlet(20): 0.913 ProbKnot: 0.716 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Mastr(20) Matthews Correlation Coefficient Murlet(20): 0.750 Mastr(20): 0.710 Sensitivity Murlet(20): 0.619 Mastr(20): 0.638 Positive Predictive Value Murlet(20): 0.913 Mastr(20): 0.793 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Fold Matthews Correlation Coefficient Murlet(20): 0.750 Fold: 0.713 Sensitivity Murlet(20): 0.619 Fold: 0.711 Positive Predictive Value Murlet(20): 0.913 Fold: 0.718 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs UNAFold Matthews Correlation Coefficient Murlet(20): 0.750 UNAFold: 0.708 Sensitivity Murlet(20): 0.619 UNAFold: 0.697 Positive Predictive Value Murlet(20): 0.913 UNAFold: 0.724 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs PknotsRG Matthews Correlation Coefficient Murlet(20): 0.750 PknotsRG: 0.692 Sensitivity Murlet(20): 0.619 PknotsRG: 0.688 Positive Predictive Value Murlet(20): 0.913 PknotsRG: 0.700 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Sfold Matthews Correlation Coefficient Murlet(20): 0.750 Sfold: 0.699 Sensitivity Murlet(20): 0.619 Sfold: 0.663 Positive Predictive Value Murlet(20): 0.913 Sfold: 0.741 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNAalifold(seed) vs Murlet(20) Matthews Correlation Coefficient RNAalifold(seed): 0.603 Murlet(20): 0.601 Sensitivity RNAalifold(seed): 0.381 Murlet(20): 0.392 Positive Predictive Value RNAalifold(seed): 0.959 Murlet(20): 0.924 Number of pairs reference - predicted secondary structure: 136 Wilcoxon single-rank test P-value: 6.93152570412e-05	+ Murlet(20) vs RNAsubopt Matthews Correlation Coefficient Murlet(20): 0.750 RNAsubopt: 0.695 Sensitivity Murlet(20): 0.619 RNAsubopt: 0.694 Positive Predictive Value Murlet(20): 0.913 RNAsubopt: 0.700 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs HotKnots Matthews Correlation Coefficient Murlet(20): 0.750 HotKnots: 0.699 Sensitivity Murlet(20): 0.619 HotKnots: 0.696 Positive Predictive Value Murlet(20): 0.913 HotKnots: 0.706 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs RNAfold Matthews Correlation Coefficient Murlet(20): 0.750 RNAfold: 0.687 Sensitivity Murlet(20): 0.619 RNAfold: 0.682 Positive Predictive Value Murlet(20): 0.913 RNAfold: 0.695 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs RNAshapes Matthews Correlation Coefficient Murlet(20): 0.750 RNAshapes: 0.694 Sensitivity Murlet(20): 0.619 RNAshapes: 0.688 Positive Predictive Value Murlet(20): 0.913 RNAshapes: 0.703 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs RNASampler(seed) Matthews Correlation Coefficient Murlet(20): 0.685 RNASampler(seed): 0.571 Sensitivity Murlet(20): 0.527 RNASampler(seed): 0.343 Positive Predictive Value Murlet(20): 0.896 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Afold Matthews Correlation Coefficient Murlet(20): 0.714 Afold: 0.643 Sensitivity Murlet(20): 0.547 Afold: 0.632 Positive Predictive Value Murlet(20): 0.935 Afold: 0.659 Number of pairs reference - predicted secondary structure: 163 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Pknots Matthews Correlation Coefficient Murlet(20): 0.780 Pknots: 0.657 Sensitivity Murlet(20): 0.685 Pknots: 0.663 Positive Predictive Value Murlet(20): 0.892 Pknots: 0.655 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs McQFold Matthews Correlation Coefficient Murlet(20): 0.750 McQFold: 0.612 Sensitivity Murlet(20): 0.619 McQFold: 0.589 Positive Predictive Value Murlet(20): 0.913 McQFold: 0.641 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Carnac(20) Matthews Correlation Coefficient Murlet(20): 0.750 Carnac(20): 0.676 Sensitivity Murlet(20): 0.619 Carnac(20): 0.501 Positive Predictive Value Murlet(20): 0.913 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs RNASLOpt Matthews Correlation Coefficient Murlet(20): 0.750 RNASLOpt: 0.640 Sensitivity Murlet(20): 0.619 RNASLOpt: 0.595 Positive Predictive Value Murlet(20): 0.913 RNASLOpt: 0.692 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Cylofold Matthews Correlation Coefficient Murlet(20): 0.751 Cylofold: 0.558 Sensitivity Murlet(20): 0.620 Cylofold: 0.544 Positive Predictive Value Murlet(20): 0.913 Cylofold: 0.578 Number of pairs reference - predicted secondary structure: 303 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Murlet(20) vs Multilign(seed) Matthews Correlation Coefficient Murlet(20): 0.568 Multilign(seed): 0.334 Sensitivity Murlet(20): 0.326 Multilign(seed): 0.186 Positive Predictive Value Murlet(20): 1.000 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ Murlet(20) vs RNAwolf Matthews Correlation Coefficient Murlet(20): 0.750 RNAwolf: 0.560 Sensitivity Murlet(20): 0.619 RNAwolf: 0.565 Positive Predictive Value Murlet(20): 0.913 RNAwolf: 0.561 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs PPfold(seed) Matthews Correlation Coefficient Murlet(20): 0.618 PPfold(seed): 0.352 Sensitivity Murlet(20): 0.412 PPfold(seed): 0.135 Positive Predictive Value Murlet(20): 0.932 PPfold(seed): 0.927 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ Murlet(20) vs Murlet(seed) Matthews Correlation Coefficient Murlet(20): 0.662 Murlet(seed): 0.636 Sensitivity Murlet(20): 0.490 Murlet(seed): 0.428 Positive Predictive Value Murlet(20): 0.900 Murlet(seed): 0.952 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 1.54918844895e-07	+ Murlet(20) vs Alterna Matthews Correlation Coefficient Murlet(20): 0.780 Alterna: 0.618 Sensitivity Murlet(20): 0.685 Alterna: 0.626 Positive Predictive Value Murlet(20): 0.892 Alterna: 0.616 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Carnac(seed) Matthews Correlation Coefficient Murlet(20): 0.664 Carnac(seed): 0.435 Sensitivity Murlet(20): 0.480 Carnac(seed): 0.211 Positive Predictive Value Murlet(20): 0.922 Carnac(seed): 0.907 Number of pairs reference - predicted secondary structure: 67 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Vsfold4 Matthews Correlation Coefficient Murlet(20): 0.750 Vsfold4: 0.503 Sensitivity Murlet(20): 0.619 Vsfold4: 0.467 Positive Predictive Value Murlet(20): 0.913 Vsfold4: 0.548 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(20): 0.609 RSpredict(seed): 0.412 Sensitivity Murlet(20): 0.404 RSpredict(seed): 0.276 Positive Predictive Value Murlet(20): 0.922 RSpredict(seed): 0.621 Number of pairs reference - predicted secondary structure: 140 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Vsfold5 Matthews Correlation Coefficient Murlet(20): 0.750 Vsfold5: 0.458 Sensitivity Murlet(20): 0.619 Vsfold5: 0.438 Positive Predictive Value Murlet(20): 0.913 Vsfold5: 0.485 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs RDfolder Matthews Correlation Coefficient Murlet(20): 0.780 RDfolder: 0.556 Sensitivity Murlet(20): 0.685 RDfolder: 0.511 Positive Predictive Value Murlet(20): 0.892 RDfolder: 0.611 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs MCFold Matthews Correlation Coefficient Murlet(20): 0.748 MCFold: 0.501 Sensitivity Murlet(20): 0.616 MCFold: 0.560 Positive Predictive Value Murlet(20): 0.911 MCFold: 0.454 Number of pairs reference - predicted secondary structure: 257 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs NanoFolder Matthews Correlation Coefficient Murlet(20): 0.712 NanoFolder: 0.337 Sensitivity Murlet(20): 0.555 NanoFolder: 0.391 Positive Predictive Value Murlet(20): 0.917 NanoFolder: 0.298 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(20) vs Mastr(seed) Matthews Correlation Coefficient Murlet(20): 0.626 Mastr(seed): 0.266 Sensitivity Murlet(20): 0.430 Mastr(seed): 0.087 Positive Predictive Value Murlet(20): 0.916 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 153 Wilcoxon single-rank test P-value: 3.56938820447e-08
CMfinder(seed)	78 ContextFold vs CMfinder(seed) Matthews Correlation Coefficient ContextFold: 0.690 CMfinder(seed): 0.571 Sensitivity ContextFold: 0.632 CMfinder(seed): 0.439 Positive Predictive Value ContextFold: 0.758 CMfinder(seed): 0.747 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 TurboFold(20) vs CMfinder(seed) Matthews Correlation Coefficient TurboFold(20): 0.744 CMfinder(seed): 0.736 Sensitivity TurboFold(20): 0.678 CMfinder(seed): 0.607 Positive Predictive Value TurboFold(20): 0.821 CMfinder(seed): 0.898 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 2.89205881697e-05	78 CentroidAlifold(seed) vs CMfinder(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.804 CMfinder(seed): 0.571 Sensitivity CentroidAlifold(seed): 0.666 CMfinder(seed): 0.439 Positive Predictive Value CentroidAlifold(seed): 0.974 CMfinder(seed): 0.747 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 CentroidHomfold‑LAST vs CMfinder(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.709 CMfinder(seed): 0.571 Sensitivity CentroidHomfold‑LAST: 0.631 CMfinder(seed): 0.439 Positive Predictive Value CentroidHomfold‑LAST: 0.801 CMfinder(seed): 0.747 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 PETfold_pre2.0(seed) vs CMfinder(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.745 CMfinder(seed): 0.571 Sensitivity PETfold_pre2.0(seed): 0.645 CMfinder(seed): 0.439 Positive Predictive Value PETfold_pre2.0(seed): 0.864 CMfinder(seed): 0.747 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 CMfinder(seed) vs TurboFold(seed) Matthews Correlation Coefficient CMfinder(seed): 0.616 TurboFold(seed): 0.607 Sensitivity CMfinder(seed): 0.481 TurboFold(seed): 0.540 Positive Predictive Value CMfinder(seed): 0.796 TurboFold(seed): 0.690 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 0.00165341959409	78 MXScarna(seed) vs CMfinder(seed) Matthews Correlation Coefficient MXScarna(seed): 0.699 CMfinder(seed): 0.571 Sensitivity MXScarna(seed): 0.663 CMfinder(seed): 0.439 Positive Predictive Value MXScarna(seed): 0.741 CMfinder(seed): 0.747 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 CentroidAlifold(20) vs CMfinder(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.805 CMfinder(seed): 0.736 Sensitivity CentroidAlifold(20): 0.718 CMfinder(seed): 0.607 Positive Predictive Value CentroidAlifold(20): 0.907 CMfinder(seed): 0.898 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.23657817852e-08	38 CMfinder(seed) vs PETfold_pre2.0(20) Matthews Correlation Coefficient CMfinder(seed): 0.736 PETfold_pre2.0(20): 0.708 Sensitivity CMfinder(seed): 0.607 PETfold_pre2.0(20): 0.594 Positive Predictive Value CMfinder(seed): 0.898 PETfold_pre2.0(20): 0.851 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.19332990918e-08	38 MXScarna(20) vs CMfinder(seed) Matthews Correlation Coefficient MXScarna(20): 0.820 CMfinder(seed): 0.736 Sensitivity MXScarna(20): 0.785 CMfinder(seed): 0.607 Positive Predictive Value MXScarna(20): 0.860 CMfinder(seed): 0.898 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 CMfinder(seed) vs PPfold(20) Matthews Correlation Coefficient CMfinder(seed): 0.736 PPfold(20): 0.656 Sensitivity CMfinder(seed): 0.607 PPfold(20): 0.507 Positive Predictive Value CMfinder(seed): 0.898 PPfold(20): 0.856 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.1503931209e-08	38 CMfinder(seed) vs RNAalifold(20) Matthews Correlation Coefficient CMfinder(seed): 0.736 RNAalifold(20): 0.620 Sensitivity CMfinder(seed): 0.607 RNAalifold(20): 0.466 Positive Predictive Value CMfinder(seed): 0.898 RNAalifold(20): 0.832 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.19332990918e-08	38 CMfinder(seed) vs RSpredict(20) Matthews Correlation Coefficient CMfinder(seed): 0.736 RSpredict(20): 0.729 Sensitivity CMfinder(seed): 0.607 RSpredict(20): 0.656 Positive Predictive Value CMfinder(seed): 0.898 RSpredict(20): 0.816 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 0.00531619474363	78 IPknot vs CMfinder(seed) Matthews Correlation Coefficient IPknot: 0.617 CMfinder(seed): 0.571 Sensitivity IPknot: 0.554 CMfinder(seed): 0.439 Positive Predictive Value IPknot: 0.692 CMfinder(seed): 0.747 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 CMfinder(seed) vs Multilign(20) Matthews Correlation Coefficient CMfinder(seed): 0.736 Multilign(20): 0.657 Sensitivity CMfinder(seed): 0.607 Multilign(20): 0.508 Positive Predictive Value CMfinder(seed): 0.898 Multilign(20): 0.856 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 CentroidFold vs CMfinder(seed) Matthews Correlation Coefficient CentroidFold: 0.599 CMfinder(seed): 0.571 Sensitivity CentroidFold: 0.514 CMfinder(seed): 0.439 Positive Predictive Value CentroidFold: 0.701 CMfinder(seed): 0.747 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.85233844192e-08	78 Contrafold vs CMfinder(seed) Matthews Correlation Coefficient Contrafold: 0.594 CMfinder(seed): 0.571 Sensitivity Contrafold: 0.546 CMfinder(seed): 0.439 Positive Predictive Value Contrafold: 0.650 CMfinder(seed): 0.747 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 4.83792096436e-08	38 CMfinder(seed) vs RNASampler(20) Matthews Correlation Coefficient CMfinder(seed): 0.736 RNASampler(20): 0.593 Sensitivity CMfinder(seed): 0.607 RNASampler(20): 0.399 Positive Predictive Value CMfinder(seed): 0.898 RNASampler(20): 0.888 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.23657817852e-08	38 CMfinder(seed) vs Murlet(20) Matthews Correlation Coefficient CMfinder(seed): 0.736 Murlet(20): 0.649 Sensitivity CMfinder(seed): 0.607 Murlet(20): 0.483 Positive Predictive Value CMfinder(seed): 0.898 Murlet(20): 0.878 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.23657817852e-08		- MaxExpect vs CMfinder(seed) Matthews Correlation Coefficient MaxExpect: 0.589 CMfinder(seed): 0.571 Sensitivity MaxExpect: 0.552 CMfinder(seed): 0.439 Positive Predictive Value MaxExpect: 0.633 CMfinder(seed): 0.747 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 1.02208072244e-07	+ CMfinder(seed) vs CMfinder(20) Matthews Correlation Coefficient CMfinder(seed): 0.736 CMfinder(20): 0.711 Sensitivity CMfinder(seed): 0.607 CMfinder(20): 0.579 Positive Predictive Value CMfinder(seed): 0.898 CMfinder(20): 0.880 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.02343278931e-08	+ CMfinder(seed) vs CRWrnafold Matthews Correlation Coefficient CMfinder(seed): 0.571 CRWrnafold: 0.445 Sensitivity CMfinder(seed): 0.439 CRWrnafold: 0.424 Positive Predictive Value CMfinder(seed): 0.747 CRWrnafold: 0.474 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	= CMfinder(seed) vs ProbKnot Matthews Correlation Coefficient CMfinder(seed): 0.571 ProbKnot: 0.564 Sensitivity CMfinder(seed): 0.439 ProbKnot: 0.536 Positive Predictive Value CMfinder(seed): 0.747 ProbKnot: 0.599 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 0.0139030957526	- Mastr(20) vs CMfinder(seed) Matthews Correlation Coefficient Mastr(20): 0.748 CMfinder(seed): 0.736 Sensitivity Mastr(20): 0.683 CMfinder(seed): 0.607 Positive Predictive Value Mastr(20): 0.824 CMfinder(seed): 0.898 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 1.35806673514e-06	= Fold vs CMfinder(seed) Matthews Correlation Coefficient Fold: 0.574 CMfinder(seed): 0.571 Sensitivity Fold: 0.550 CMfinder(seed): 0.439 Positive Predictive Value Fold: 0.603 CMfinder(seed): 0.747 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 0.518809073978	- UNAFold vs CMfinder(seed) Matthews Correlation Coefficient UNAFold: 0.581 CMfinder(seed): 0.571 Sensitivity UNAFold: 0.556 CMfinder(seed): 0.439 Positive Predictive Value UNAFold: 0.613 CMfinder(seed): 0.747 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 2.90292419552e-06	- PknotsRG vs CMfinder(seed) Matthews Correlation Coefficient PknotsRG: 0.598 CMfinder(seed): 0.571 Sensitivity PknotsRG: 0.582 CMfinder(seed): 0.439 Positive Predictive Value PknotsRG: 0.619 CMfinder(seed): 0.747 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 5.21776328505e-08	+ CMfinder(seed) vs Sfold Matthews Correlation Coefficient CMfinder(seed): 0.571 Sfold: 0.545 Sensitivity CMfinder(seed): 0.439 Sfold: 0.497 Positive Predictive Value CMfinder(seed): 0.747 Sfold: 0.604 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 5.62644058675e-08	- RNAalifold(seed) vs CMfinder(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.654 CMfinder(seed): 0.571 Sensitivity RNAalifold(seed): 0.499 CMfinder(seed): 0.439 Positive Predictive Value RNAalifold(seed): 0.860 CMfinder(seed): 0.747 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(seed) vs RNAsubopt Matthews Correlation Coefficient CMfinder(seed): 0.571 RNAsubopt: 0.527 Sensitivity CMfinder(seed): 0.439 RNAsubopt: 0.511 Positive Predictive Value CMfinder(seed): 0.747 RNAsubopt: 0.549 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(seed) vs HotKnots Matthews Correlation Coefficient CMfinder(seed): 0.593 HotKnots: 0.499 Sensitivity CMfinder(seed): 0.459 HotKnots: 0.488 Positive Predictive Value CMfinder(seed): 0.771 HotKnots: 0.517 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(seed) vs RNAfold Matthews Correlation Coefficient CMfinder(seed): 0.571 RNAfold: 0.545 Sensitivity CMfinder(seed): 0.439 RNAfold: 0.524 Positive Predictive Value CMfinder(seed): 0.747 RNAfold: 0.572 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(seed) vs RNAshapes Matthews Correlation Coefficient CMfinder(seed): 0.571 RNAshapes: 0.539 Sensitivity CMfinder(seed): 0.439 RNAshapes: 0.519 Positive Predictive Value CMfinder(seed): 0.747 RNAshapes: 0.565 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(seed) vs RNASampler(seed) Matthews Correlation Coefficient CMfinder(seed): 0.571 RNASampler(seed): 0.554 Sensitivity CMfinder(seed): 0.439 RNASampler(seed): 0.388 Positive Predictive Value CMfinder(seed): 0.747 RNASampler(seed): 0.795 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 7.04732813174e-08	+ CMfinder(seed) vs Afold Matthews Correlation Coefficient CMfinder(seed): 0.590 Afold: 0.573 Sensitivity CMfinder(seed): 0.463 Afold: 0.557 Positive Predictive Value CMfinder(seed): 0.758 Afold: 0.594 Number of pairs reference - predicted secondary structure: 71 Wilcoxon single-rank test P-value: 8.1815824276e-08	+ CMfinder(seed) vs Pknots Matthews Correlation Coefficient CMfinder(seed): 0.512 Pknots: 0.398 Sensitivity CMfinder(seed): 0.382 Pknots: 0.381 Positive Predictive Value CMfinder(seed): 0.696 Pknots: 0.429 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(seed) vs McQFold Matthews Correlation Coefficient CMfinder(seed): 0.571 McQFold: 0.536 Sensitivity CMfinder(seed): 0.439 McQFold: 0.489 Positive Predictive Value CMfinder(seed): 0.747 McQFold: 0.593 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(seed) vs Carnac(20) Matthews Correlation Coefficient CMfinder(seed): 0.736 Carnac(20): 0.413 Sensitivity CMfinder(seed): 0.607 Carnac(20): 0.190 Positive Predictive Value CMfinder(seed): 0.898 Carnac(20): 0.911 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 4.39131584674e-08	+ CMfinder(seed) vs RNASLOpt Matthews Correlation Coefficient CMfinder(seed): 0.571 RNASLOpt: 0.504 Sensitivity CMfinder(seed): 0.439 RNASLOpt: 0.440 Positive Predictive Value CMfinder(seed): 0.747 RNASLOpt: 0.582 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(seed) vs Cylofold Matthews Correlation Coefficient CMfinder(seed): 0.599 Cylofold: 0.465 Sensitivity CMfinder(seed): 0.469 Cylofold: 0.415 Positive Predictive Value CMfinder(seed): 0.772 Cylofold: 0.531 Number of pairs reference - predicted secondary structure: 67 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(seed) vs Multilign(seed) Matthews Correlation Coefficient CMfinder(seed): 0.497 Multilign(seed): 0.444 Sensitivity CMfinder(seed): 0.354 Multilign(seed): 0.335 Positive Predictive Value CMfinder(seed): 0.707 Multilign(seed): 0.598 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 5.70361883708e-09	+ CMfinder(seed) vs RNAwolf Matthews Correlation Coefficient CMfinder(seed): 0.571 RNAwolf: 0.369 Sensitivity CMfinder(seed): 0.439 RNAwolf: 0.369 Positive Predictive Value CMfinder(seed): 0.747 RNAwolf: 0.377 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	- PPfold(seed) vs CMfinder(seed) Matthews Correlation Coefficient PPfold(seed): 0.600 CMfinder(seed): 0.585 Sensitivity PPfold(seed): 0.455 CMfinder(seed): 0.440 Positive Predictive Value PPfold(seed): 0.798 CMfinder(seed): 0.786 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.60044567142e-05	+ CMfinder(seed) vs Murlet(seed) Matthews Correlation Coefficient CMfinder(seed): 0.571 Murlet(seed): 0.488 Sensitivity CMfinder(seed): 0.439 Murlet(seed): 0.291 Positive Predictive Value CMfinder(seed): 0.747 Murlet(seed): 0.824 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(seed) vs Alterna Matthews Correlation Coefficient CMfinder(seed): 0.512 Alterna: 0.405 Sensitivity CMfinder(seed): 0.382 Alterna: 0.380 Positive Predictive Value CMfinder(seed): 0.696 Alterna: 0.445 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(seed) vs Carnac(seed) Matthews Correlation Coefficient CMfinder(seed): 0.571 Carnac(seed): 0.422 Sensitivity CMfinder(seed): 0.439 Carnac(seed): 0.216 Positive Predictive Value CMfinder(seed): 0.747 Carnac(seed): 0.830 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(seed) vs Vsfold4 Matthews Correlation Coefficient CMfinder(seed): 0.571 Vsfold4: 0.403 Sensitivity CMfinder(seed): 0.439 Vsfold4: 0.355 Positive Predictive Value CMfinder(seed): 0.747 Vsfold4: 0.464 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(seed) vs RSpredict(seed) Matthews Correlation Coefficient CMfinder(seed): 0.571 RSpredict(seed): 0.512 Sensitivity CMfinder(seed): 0.439 RSpredict(seed): 0.408 Positive Predictive Value CMfinder(seed): 0.747 RSpredict(seed): 0.649 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(seed) vs Vsfold5 Matthews Correlation Coefficient CMfinder(seed): 0.571 Vsfold5: 0.383 Sensitivity CMfinder(seed): 0.439 Vsfold5: 0.348 Positive Predictive Value CMfinder(seed): 0.747 Vsfold5: 0.428 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(seed) vs RDfolder Matthews Correlation Coefficient CMfinder(seed): 0.512 RDfolder: 0.317 Sensitivity CMfinder(seed): 0.382 RDfolder: 0.254 Positive Predictive Value CMfinder(seed): 0.696 RDfolder: 0.411 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(seed) vs MCFold Matthews Correlation Coefficient CMfinder(seed): 0.555 MCFold: 0.396 Sensitivity CMfinder(seed): 0.421 MCFold: 0.436 Positive Predictive Value CMfinder(seed): 0.736 MCFold: 0.367 Number of pairs reference - predicted secondary structure: 68 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(seed) vs NanoFolder Matthews Correlation Coefficient CMfinder(seed): 0.575 NanoFolder: 0.392 Sensitivity CMfinder(seed): 0.432 NanoFolder: 0.436 Positive Predictive Value CMfinder(seed): 0.771 NanoFolder: 0.362 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.82627677697e-08	+ CMfinder(seed) vs Mastr(seed) Matthews Correlation Coefficient CMfinder(seed): 0.571 Mastr(seed): 0.504 Sensitivity CMfinder(seed): 0.439 Mastr(seed): 0.320 Positive Predictive Value CMfinder(seed): 0.747 Mastr(seed): 0.798 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08
MaxExpect	882 ContextFold vs MaxExpect Matthews Correlation Coefficient ContextFold: 0.779 MaxExpect: 0.633 Sensitivity ContextFold: 0.741 MaxExpect: 0.617 Positive Predictive Value ContextFold: 0.823 MaxExpect: 0.654 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 TurboFold(20) vs MaxExpect Matthews Correlation Coefficient TurboFold(20): 0.889 MaxExpect: 0.711 Sensitivity TurboFold(20): 0.861 MaxExpect: 0.701 Positive Predictive Value TurboFold(20): 0.919 MaxExpect: 0.725 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	216 CentroidAlifold(seed) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(seed): 0.790 MaxExpect: 0.694 Sensitivity CentroidAlifold(seed): 0.699 MaxExpect: 0.684 Positive Predictive Value CentroidAlifold(seed): 0.896 MaxExpect: 0.707 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 CentroidHomfold‑LAST vs MaxExpect Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.736 MaxExpect: 0.633 Sensitivity CentroidHomfold‑LAST: 0.665 MaxExpect: 0.617 Positive Predictive Value CentroidHomfold‑LAST: 0.818 MaxExpect: 0.654 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	498 PETfold_pre2.0(seed) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.879 MaxExpect: 0.694 Sensitivity PETfold_pre2.0(seed): 0.825 MaxExpect: 0.685 Positive Predictive Value PETfold_pre2.0(seed): 0.938 MaxExpect: 0.706 Number of pairs reference - predicted secondary structure: 498 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 TurboFold(seed) vs MaxExpect Matthews Correlation Coefficient TurboFold(seed): 0.798 MaxExpect: 0.762 Sensitivity TurboFold(seed): 0.766 MaxExpect: 0.750 Positive Predictive Value TurboFold(seed): 0.835 MaxExpect: 0.778 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	233 MXScarna(seed) vs MaxExpect Matthews Correlation Coefficient MXScarna(seed): 0.750 MaxExpect: 0.691 Sensitivity MXScarna(seed): 0.712 MaxExpect: 0.680 Positive Predictive Value MXScarna(seed): 0.793 MaxExpect: 0.705 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 CentroidAlifold(20) vs MaxExpect Matthews Correlation Coefficient CentroidAlifold(20): 0.849 MaxExpect: 0.711 Sensitivity CentroidAlifold(20): 0.754 MaxExpect: 0.701 Positive Predictive Value CentroidAlifold(20): 0.957 MaxExpect: 0.725 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 PETfold_pre2.0(20) vs MaxExpect Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 MaxExpect: 0.711 Sensitivity PETfold_pre2.0(20): 0.737 MaxExpect: 0.701 Positive Predictive Value PETfold_pre2.0(20): 0.975 MaxExpect: 0.725 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 MXScarna(20) vs MaxExpect Matthews Correlation Coefficient MXScarna(20): 0.838 MaxExpect: 0.711 Sensitivity MXScarna(20): 0.791 MaxExpect: 0.701 Positive Predictive Value MXScarna(20): 0.891 MaxExpect: 0.725 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	314 PPfold(20) vs MaxExpect Matthews Correlation Coefficient PPfold(20): 0.839 MaxExpect: 0.709 Sensitivity PPfold(20): 0.721 MaxExpect: 0.698 Positive Predictive Value PPfold(20): 0.977 MaxExpect: 0.723 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RNAalifold(20) vs MaxExpect Matthews Correlation Coefficient RNAalifold(20): 0.816 MaxExpect: 0.711 Sensitivity RNAalifold(20): 0.690 MaxExpect: 0.701 Positive Predictive Value RNAalifold(20): 0.966 MaxExpect: 0.725 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RSpredict(20) vs MaxExpect Matthews Correlation Coefficient RSpredict(20): 0.789 MaxExpect: 0.711 Sensitivity RSpredict(20): 0.693 MaxExpect: 0.701 Positive Predictive Value RSpredict(20): 0.901 MaxExpect: 0.725 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 IPknot vs MaxExpect Matthews Correlation Coefficient IPknot: 0.694 MaxExpect: 0.633 Sensitivity IPknot: 0.661 MaxExpect: 0.617 Positive Predictive Value IPknot: 0.733 MaxExpect: 0.654 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	311 Multilign(20) vs MaxExpect Matthews Correlation Coefficient Multilign(20): 0.784 MaxExpect: 0.710 Sensitivity Multilign(20): 0.697 MaxExpect: 0.700 Positive Predictive Value Multilign(20): 0.885 MaxExpect: 0.725 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 CentroidFold vs MaxExpect Matthews Correlation Coefficient CentroidFold: 0.645 MaxExpect: 0.633 Sensitivity CentroidFold: 0.612 MaxExpect: 0.617 Positive Predictive Value CentroidFold: 0.684 MaxExpect: 0.654 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 Contrafold vs MaxExpect Matthews Correlation Coefficient Contrafold: 0.643 MaxExpect: 0.633 Sensitivity Contrafold: 0.634 MaxExpect: 0.617 Positive Predictive Value Contrafold: 0.657 MaxExpect: 0.654 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	315 RNASampler(20) vs MaxExpect Matthews Correlation Coefficient RNASampler(20): 0.770 MaxExpect: 0.714 Sensitivity RNASampler(20): 0.622 MaxExpect: 0.703 Positive Predictive Value RNASampler(20): 0.957 MaxExpect: 0.728 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	319 Murlet(20) vs MaxExpect Matthews Correlation Coefficient Murlet(20): 0.750 MaxExpect: 0.712 Sensitivity Murlet(20): 0.619 MaxExpect: 0.702 Positive Predictive Value Murlet(20): 0.913 MaxExpect: 0.726 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 MaxExpect vs CMfinder(seed) Matthews Correlation Coefficient MaxExpect: 0.589 CMfinder(seed): 0.571 Sensitivity MaxExpect: 0.552 CMfinder(seed): 0.439 Positive Predictive Value MaxExpect: 0.633 CMfinder(seed): 0.747 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 1.02208072244e-07		- CMfinder(20) vs MaxExpect Matthews Correlation Coefficient CMfinder(20): 0.735 MaxExpect: 0.711 Sensitivity CMfinder(20): 0.603 MaxExpect: 0.701 Positive Predictive Value CMfinder(20): 0.899 MaxExpect: 0.724 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs CRWrnafold Matthews Correlation Coefficient MaxExpect: 0.633 CRWrnafold: 0.630 Sensitivity MaxExpect: 0.617 CRWrnafold: 0.618 Positive Predictive Value MaxExpect: 0.654 CRWrnafold: 0.648 Number of pairs reference - predicted secondary structure: 881 Wilcoxon single-rank test P-value: 3.90487810335e-05	+ MaxExpect vs ProbKnot Matthews Correlation Coefficient MaxExpect: 0.633 ProbKnot: 0.630 Sensitivity MaxExpect: 0.617 ProbKnot: 0.622 Positive Predictive Value MaxExpect: 0.654 ProbKnot: 0.644 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	= MaxExpect vs Mastr(20) Matthews Correlation Coefficient MaxExpect: 0.711 Mastr(20): 0.708 Sensitivity MaxExpect: 0.701 Mastr(20): 0.635 Positive Predictive Value MaxExpect: 0.725 Mastr(20): 0.793 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 0.0256642192469	+ MaxExpect vs Fold Matthews Correlation Coefficient MaxExpect: 0.633 Fold: 0.628 Sensitivity MaxExpect: 0.617 Fold: 0.620 Positive Predictive Value MaxExpect: 0.654 Fold: 0.641 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs UNAFold Matthews Correlation Coefficient MaxExpect: 0.633 UNAFold: 0.620 Sensitivity MaxExpect: 0.617 UNAFold: 0.605 Positive Predictive Value MaxExpect: 0.654 UNAFold: 0.639 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs PknotsRG Matthews Correlation Coefficient MaxExpect: 0.633 PknotsRG: 0.617 Sensitivity MaxExpect: 0.617 PknotsRG: 0.610 Positive Predictive Value MaxExpect: 0.654 PknotsRG: 0.630 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Sfold Matthews Correlation Coefficient MaxExpect: 0.633 Sfold: 0.618 Sensitivity MaxExpect: 0.617 Sfold: 0.581 Positive Predictive Value MaxExpect: 0.654 Sfold: 0.663 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNAalifold(seed) Matthews Correlation Coefficient MaxExpect: 0.695 RNAalifold(seed): 0.610 Sensitivity MaxExpect: 0.684 RNAalifold(seed): 0.404 Positive Predictive Value MaxExpect: 0.710 RNAalifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNAsubopt Matthews Correlation Coefficient MaxExpect: 0.633 RNAsubopt: 0.615 Sensitivity MaxExpect: 0.617 RNAsubopt: 0.609 Positive Predictive Value MaxExpect: 0.654 RNAsubopt: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs HotKnots Matthews Correlation Coefficient MaxExpect: 0.634 HotKnots: 0.613 Sensitivity MaxExpect: 0.618 HotKnots: 0.607 Positive Predictive Value MaxExpect: 0.656 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 875 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNAfold Matthews Correlation Coefficient MaxExpect: 0.633 RNAfold: 0.612 Sensitivity MaxExpect: 0.617 RNAfold: 0.604 Positive Predictive Value MaxExpect: 0.654 RNAfold: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNAshapes Matthews Correlation Coefficient MaxExpect: 0.633 RNAshapes: 0.612 Sensitivity MaxExpect: 0.617 RNAshapes: 0.602 Positive Predictive Value MaxExpect: 0.654 RNAshapes: 0.628 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNASampler(seed) Matthews Correlation Coefficient MaxExpect: 0.604 RNASampler(seed): 0.557 Sensitivity MaxExpect: 0.567 RNASampler(seed): 0.389 Positive Predictive Value MaxExpect: 0.648 RNASampler(seed): 0.802 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Afold Matthews Correlation Coefficient MaxExpect: 0.622 Afold: 0.558 Sensitivity MaxExpect: 0.596 Afold: 0.541 Positive Predictive Value MaxExpect: 0.654 Afold: 0.582 Number of pairs reference - predicted secondary structure: 530 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Pknots Matthews Correlation Coefficient MaxExpect: 0.640 Pknots: 0.606 Sensitivity MaxExpect: 0.621 Pknots: 0.595 Positive Predictive Value MaxExpect: 0.666 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs McQFold Matthews Correlation Coefficient MaxExpect: 0.633 McQFold: 0.583 Sensitivity MaxExpect: 0.617 McQFold: 0.557 Positive Predictive Value MaxExpect: 0.654 McQFold: 0.616 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Carnac(20) Matthews Correlation Coefficient MaxExpect: 0.711 Carnac(20): 0.675 Sensitivity MaxExpect: 0.701 Carnac(20): 0.500 Positive Predictive Value MaxExpect: 0.725 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RNASLOpt Matthews Correlation Coefficient MaxExpect: 0.633 RNASLOpt: 0.562 Sensitivity MaxExpect: 0.617 RNASLOpt: 0.521 Positive Predictive Value MaxExpect: 0.654 RNASLOpt: 0.613 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Cylofold Matthews Correlation Coefficient MaxExpect: 0.660 Cylofold: 0.577 Sensitivity MaxExpect: 0.642 Cylofold: 0.554 Positive Predictive Value MaxExpect: 0.684 Cylofold: 0.608 Number of pairs reference - predicted secondary structure: 796 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Multilign(seed) Matthews Correlation Coefficient MaxExpect: 0.497 Multilign(seed): 0.485 Sensitivity MaxExpect: 0.456 Multilign(seed): 0.386 Positive Predictive Value MaxExpect: 0.551 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.14576075128e-05	+ MaxExpect vs RNAwolf Matthews Correlation Coefficient MaxExpect: 0.633 RNAwolf: 0.518 Sensitivity MaxExpect: 0.617 RNAwolf: 0.523 Positive Predictive Value MaxExpect: 0.654 RNAwolf: 0.520 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs PPfold(seed) Matthews Correlation Coefficient MaxExpect: 0.736 PPfold(seed): 0.380 Sensitivity MaxExpect: 0.730 PPfold(seed): 0.170 Positive Predictive Value MaxExpect: 0.746 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Murlet(seed) Matthews Correlation Coefficient MaxExpect: 0.636 Murlet(seed): 0.468 Sensitivity MaxExpect: 0.602 Murlet(seed): 0.266 Positive Predictive Value MaxExpect: 0.676 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Alterna Matthews Correlation Coefficient MaxExpect: 0.641 Alterna: 0.552 Sensitivity MaxExpect: 0.622 Alterna: 0.547 Positive Predictive Value MaxExpect: 0.667 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Carnac(seed) Matthews Correlation Coefficient MaxExpect: 0.667 Carnac(seed): 0.415 Sensitivity MaxExpect: 0.644 Carnac(seed): 0.196 Positive Predictive Value MaxExpect: 0.695 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Vsfold4 Matthews Correlation Coefficient MaxExpect: 0.633 Vsfold4: 0.487 Sensitivity MaxExpect: 0.617 Vsfold4: 0.447 Positive Predictive Value MaxExpect: 0.654 Vsfold4: 0.537 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RSpredict(seed) Matthews Correlation Coefficient MaxExpect: 0.694 RSpredict(seed): 0.373 Sensitivity MaxExpect: 0.684 RSpredict(seed): 0.251 Positive Predictive Value MaxExpect: 0.707 RSpredict(seed): 0.562 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Vsfold5 Matthews Correlation Coefficient MaxExpect: 0.633 Vsfold5: 0.477 Sensitivity MaxExpect: 0.617 Vsfold5: 0.450 Positive Predictive Value MaxExpect: 0.654 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs RDfolder Matthews Correlation Coefficient MaxExpect: 0.641 RDfolder: 0.520 Sensitivity MaxExpect: 0.622 RDfolder: 0.464 Positive Predictive Value MaxExpect: 0.667 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs MCFold Matthews Correlation Coefficient MaxExpect: 0.642 MCFold: 0.473 Sensitivity MaxExpect: 0.623 MCFold: 0.524 Positive Predictive Value MaxExpect: 0.666 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs NanoFolder Matthews Correlation Coefficient MaxExpect: 0.668 NanoFolder: 0.335 Sensitivity MaxExpect: 0.650 NanoFolder: 0.384 Positive Predictive Value MaxExpect: 0.691 NanoFolder: 0.301 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MaxExpect vs Mastr(seed) Matthews Correlation Coefficient MaxExpect: 0.691 Mastr(seed): 0.263 Sensitivity MaxExpect: 0.680 Mastr(seed): 0.089 Positive Predictive Value MaxExpect: 0.705 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08
CMfinder(20)	316 ContextFold vs CMfinder(20) Matthews Correlation Coefficient ContextFold: 0.922 CMfinder(20): 0.735 Sensitivity ContextFold: 0.898 CMfinder(20): 0.603 Positive Predictive Value ContextFold: 0.949 CMfinder(20): 0.899 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	316 TurboFold(20) vs CMfinder(20) Matthews Correlation Coefficient TurboFold(20): 0.890 CMfinder(20): 0.735 Sensitivity TurboFold(20): 0.862 CMfinder(20): 0.603 Positive Predictive Value TurboFold(20): 0.920 CMfinder(20): 0.899 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	137 CentroidAlifold(seed) vs CMfinder(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.816 CMfinder(20): 0.649 Sensitivity CentroidAlifold(seed): 0.744 CMfinder(20): 0.500 Positive Predictive Value CentroidAlifold(seed): 0.896 CMfinder(20): 0.846 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 3.56938820447e-08	316 CentroidHomfold‑LAST vs CMfinder(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.859 CMfinder(20): 0.735 Sensitivity CentroidHomfold‑LAST: 0.822 CMfinder(20): 0.603 Positive Predictive Value CentroidHomfold‑LAST: 0.900 CMfinder(20): 0.899 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	315 PETfold_pre2.0(seed) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.888 CMfinder(20): 0.735 Sensitivity PETfold_pre2.0(seed): 0.837 CMfinder(20): 0.603 Positive Predictive Value PETfold_pre2.0(seed): 0.945 CMfinder(20): 0.899 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 TurboFold(seed) vs CMfinder(20) Matthews Correlation Coefficient TurboFold(seed): 0.880 CMfinder(20): 0.693 Sensitivity TurboFold(seed): 0.875 CMfinder(20): 0.551 Positive Predictive Value TurboFold(seed): 0.886 CMfinder(20): 0.875 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.80908287419e-08	149 MXScarna(seed) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(seed): 0.795 CMfinder(20): 0.664 Sensitivity MXScarna(seed): 0.760 CMfinder(20): 0.517 Positive Predictive Value MXScarna(seed): 0.834 CMfinder(20): 0.857 Number of pairs reference - predicted secondary structure: 149 Wilcoxon single-rank test P-value: 3.56938820447e-08	316 CentroidAlifold(20) vs CMfinder(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.854 CMfinder(20): 0.735 Sensitivity CentroidAlifold(20): 0.763 CMfinder(20): 0.603 Positive Predictive Value CentroidAlifold(20): 0.957 CMfinder(20): 0.899 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	316 PETfold_pre2.0(20) vs CMfinder(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.852 CMfinder(20): 0.735 Sensitivity PETfold_pre2.0(20): 0.746 CMfinder(20): 0.603 Positive Predictive Value PETfold_pre2.0(20): 0.975 CMfinder(20): 0.899 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	316 MXScarna(20) vs CMfinder(20) Matthews Correlation Coefficient MXScarna(20): 0.843 CMfinder(20): 0.735 Sensitivity MXScarna(20): 0.800 CMfinder(20): 0.603 Positive Predictive Value MXScarna(20): 0.890 CMfinder(20): 0.899 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	311 PPfold(20) vs CMfinder(20) Matthews Correlation Coefficient PPfold(20): 0.843 CMfinder(20): 0.737 Sensitivity PPfold(20): 0.729 CMfinder(20): 0.607 Positive Predictive Value PPfold(20): 0.977 CMfinder(20): 0.898 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	316 RNAalifold(20) vs CMfinder(20) Matthews Correlation Coefficient RNAalifold(20): 0.820 CMfinder(20): 0.735 Sensitivity RNAalifold(20): 0.698 CMfinder(20): 0.603 Positive Predictive Value RNAalifold(20): 0.966 CMfinder(20): 0.899 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	316 RSpredict(20) vs CMfinder(20) Matthews Correlation Coefficient RSpredict(20): 0.796 CMfinder(20): 0.735 Sensitivity RSpredict(20): 0.705 CMfinder(20): 0.603 Positive Predictive Value RSpredict(20): 0.902 CMfinder(20): 0.899 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	316 IPknot vs CMfinder(20) Matthews Correlation Coefficient IPknot: 0.781 CMfinder(20): 0.735 Sensitivity IPknot: 0.760 CMfinder(20): 0.603 Positive Predictive Value IPknot: 0.806 CMfinder(20): 0.899 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	307 Multilign(20) vs CMfinder(20) Matthews Correlation Coefficient Multilign(20): 0.790 CMfinder(20): 0.742 Sensitivity Multilign(20): 0.706 CMfinder(20): 0.613 Positive Predictive Value Multilign(20): 0.887 CMfinder(20): 0.901 Number of pairs reference - predicted secondary structure: 307 Wilcoxon single-rank test P-value: 3.56938820447e-08	316 CMfinder(20) vs CentroidFold Matthews Correlation Coefficient CMfinder(20): 0.735 CentroidFold: 0.734 Sensitivity CMfinder(20): 0.603 CentroidFold: 0.709 Positive Predictive Value CMfinder(20): 0.899 CentroidFold: 0.763 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 0.27038065226	316 CMfinder(20) vs Contrafold Matthews Correlation Coefficient CMfinder(20): 0.735 Contrafold: 0.732 Sensitivity CMfinder(20): 0.603 Contrafold: 0.728 Positive Predictive Value CMfinder(20): 0.899 Contrafold: 0.739 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 0.0124164808574	311 RNASampler(20) vs CMfinder(20) Matthews Correlation Coefficient RNASampler(20): 0.775 CMfinder(20): 0.736 Sensitivity RNASampler(20): 0.629 CMfinder(20): 0.605 Positive Predictive Value RNASampler(20): 0.957 CMfinder(20): 0.898 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	315 Murlet(20) vs CMfinder(20) Matthews Correlation Coefficient Murlet(20): 0.754 CMfinder(20): 0.735 Sensitivity Murlet(20): 0.626 CMfinder(20): 0.603 Positive Predictive Value Murlet(20): 0.913 CMfinder(20): 0.899 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 CMfinder(seed) vs CMfinder(20) Matthews Correlation Coefficient CMfinder(seed): 0.736 CMfinder(20): 0.711 Sensitivity CMfinder(seed): 0.607 CMfinder(20): 0.579 Positive Predictive Value CMfinder(seed): 0.898 CMfinder(20): 0.880 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 5.02343278931e-08	316 CMfinder(20) vs MaxExpect Matthews Correlation Coefficient CMfinder(20): 0.735 MaxExpect: 0.711 Sensitivity CMfinder(20): 0.603 MaxExpect: 0.701 Positive Predictive Value CMfinder(20): 0.899 MaxExpect: 0.724 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08		- CRWrnafold vs CMfinder(20) Matthews Correlation Coefficient CRWrnafold: 0.781 CMfinder(20): 0.735 Sensitivity CRWrnafold: 0.769 CMfinder(20): 0.603 Positive Predictive Value CRWrnafold: 0.796 CMfinder(20): 0.899 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs ProbKnot Matthews Correlation Coefficient CMfinder(20): 0.735 ProbKnot: 0.706 Sensitivity CMfinder(20): 0.603 ProbKnot: 0.702 Positive Predictive Value CMfinder(20): 0.899 ProbKnot: 0.715 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs Mastr(20) Matthews Correlation Coefficient CMfinder(20): 0.735 Mastr(20): 0.712 Sensitivity CMfinder(20): 0.603 Mastr(20): 0.643 Positive Predictive Value CMfinder(20): 0.899 Mastr(20): 0.792 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs Fold Matthews Correlation Coefficient CMfinder(20): 0.735 Fold: 0.711 Sensitivity CMfinder(20): 0.603 Fold: 0.710 Positive Predictive Value CMfinder(20): 0.899 Fold: 0.716 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs UNAFold Matthews Correlation Coefficient CMfinder(20): 0.735 UNAFold: 0.707 Sensitivity CMfinder(20): 0.603 UNAFold: 0.696 Positive Predictive Value CMfinder(20): 0.899 UNAFold: 0.722 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs PknotsRG Matthews Correlation Coefficient CMfinder(20): 0.735 PknotsRG: 0.689 Sensitivity CMfinder(20): 0.603 PknotsRG: 0.685 Positive Predictive Value CMfinder(20): 0.899 PknotsRG: 0.696 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs Sfold Matthews Correlation Coefficient CMfinder(20): 0.735 Sfold: 0.698 Sensitivity CMfinder(20): 0.603 Sfold: 0.662 Positive Predictive Value CMfinder(20): 0.899 Sfold: 0.739 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs RNAalifold(seed) Matthews Correlation Coefficient CMfinder(20): 0.642 RNAalifold(seed): 0.608 Sensitivity CMfinder(20): 0.492 RNAalifold(seed): 0.389 Positive Predictive Value CMfinder(20): 0.844 RNAalifold(seed): 0.954 Number of pairs reference - predicted secondary structure: 133 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs RNAsubopt Matthews Correlation Coefficient CMfinder(20): 0.735 RNAsubopt: 0.692 Sensitivity CMfinder(20): 0.603 RNAsubopt: 0.691 Positive Predictive Value CMfinder(20): 0.899 RNAsubopt: 0.697 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs HotKnots Matthews Correlation Coefficient CMfinder(20): 0.735 HotKnots: 0.696 Sensitivity CMfinder(20): 0.603 HotKnots: 0.693 Positive Predictive Value CMfinder(20): 0.899 HotKnots: 0.703 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs RNAfold Matthews Correlation Coefficient CMfinder(20): 0.735 RNAfold: 0.684 Sensitivity CMfinder(20): 0.603 RNAfold: 0.679 Positive Predictive Value CMfinder(20): 0.899 RNAfold: 0.692 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs RNAshapes Matthews Correlation Coefficient CMfinder(20): 0.735 RNAshapes: 0.693 Sensitivity CMfinder(20): 0.603 RNAshapes: 0.688 Positive Predictive Value CMfinder(20): 0.899 RNAshapes: 0.702 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs RNASampler(seed) Matthews Correlation Coefficient CMfinder(20): 0.735 RNASampler(seed): 0.571 Sensitivity CMfinder(20): 0.607 RNASampler(seed): 0.343 Positive Predictive Value CMfinder(20): 0.894 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs Afold Matthews Correlation Coefficient CMfinder(20): 0.691 Afold: 0.642 Sensitivity CMfinder(20): 0.557 Afold: 0.630 Positive Predictive Value CMfinder(20): 0.861 Afold: 0.658 Number of pairs reference - predicted secondary structure: 161 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs Pknots Matthews Correlation Coefficient CMfinder(20): 0.791 Pknots: 0.655 Sensitivity CMfinder(20): 0.678 Pknots: 0.662 Positive Predictive Value CMfinder(20): 0.926 Pknots: 0.653 Number of pairs reference - predicted secondary structure: 212 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs McQFold Matthews Correlation Coefficient CMfinder(20): 0.735 McQFold: 0.611 Sensitivity CMfinder(20): 0.603 McQFold: 0.588 Positive Predictive Value CMfinder(20): 0.899 McQFold: 0.639 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs Carnac(20) Matthews Correlation Coefficient CMfinder(20): 0.735 Carnac(20): 0.681 Sensitivity CMfinder(20): 0.603 Carnac(20): 0.508 Positive Predictive Value CMfinder(20): 0.899 Carnac(20): 0.917 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs RNASLOpt Matthews Correlation Coefficient CMfinder(20): 0.735 RNASLOpt: 0.638 Sensitivity CMfinder(20): 0.603 RNASLOpt: 0.594 Positive Predictive Value CMfinder(20): 0.899 RNASLOpt: 0.690 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs Cylofold Matthews Correlation Coefficient CMfinder(20): 0.741 Cylofold: 0.559 Sensitivity CMfinder(20): 0.610 Cylofold: 0.546 Positive Predictive Value CMfinder(20): 0.903 Cylofold: 0.578 Number of pairs reference - predicted secondary structure: 300 Wilcoxon single-rank test P-value: 3.56938820447e-08	? CMfinder(20) vs Multilign(seed) Matthews Correlation Coefficient CMfinder(20): 0.514 Multilign(seed): 0.334 Sensitivity CMfinder(20): 0.395 Multilign(seed): 0.186 Positive Predictive Value CMfinder(20): 0.680 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ CMfinder(20) vs RNAwolf Matthews Correlation Coefficient CMfinder(20): 0.735 RNAwolf: 0.563 Sensitivity CMfinder(20): 0.603 RNAwolf: 0.568 Positive Predictive Value CMfinder(20): 0.899 RNAwolf: 0.563 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs PPfold(seed) Matthews Correlation Coefficient CMfinder(20): 0.740 PPfold(seed): 0.344 Sensitivity CMfinder(20): 0.595 PPfold(seed): 0.128 Positive Predictive Value CMfinder(20): 0.924 PPfold(seed): 0.927 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 4.94031556815e-08	+ CMfinder(20) vs Murlet(seed) Matthews Correlation Coefficient CMfinder(20): 0.745 Murlet(seed): 0.636 Sensitivity CMfinder(20): 0.621 Murlet(seed): 0.428 Positive Predictive Value CMfinder(20): 0.899 Murlet(seed): 0.952 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs Alterna Matthews Correlation Coefficient CMfinder(20): 0.792 Alterna: 0.618 Sensitivity CMfinder(20): 0.679 Alterna: 0.626 Positive Predictive Value CMfinder(20): 0.927 Alterna: 0.616 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs Carnac(seed) Matthews Correlation Coefficient CMfinder(20): 0.717 Carnac(seed): 0.431 Sensitivity CMfinder(20): 0.575 Carnac(seed): 0.206 Positive Predictive Value CMfinder(20): 0.898 Carnac(seed): 0.907 Number of pairs reference - predicted secondary structure: 68 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs Vsfold4 Matthews Correlation Coefficient CMfinder(20): 0.735 Vsfold4: 0.507 Sensitivity CMfinder(20): 0.603 Vsfold4: 0.472 Positive Predictive Value CMfinder(20): 0.899 Vsfold4: 0.551 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs RSpredict(seed) Matthews Correlation Coefficient CMfinder(20): 0.649 RSpredict(seed): 0.427 Sensitivity CMfinder(20): 0.500 RSpredict(seed): 0.290 Positive Predictive Value CMfinder(20): 0.846 RSpredict(seed): 0.636 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs Vsfold5 Matthews Correlation Coefficient CMfinder(20): 0.735 Vsfold5: 0.462 Sensitivity CMfinder(20): 0.603 Vsfold5: 0.443 Positive Predictive Value CMfinder(20): 0.899 Vsfold5: 0.489 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs RDfolder Matthews Correlation Coefficient CMfinder(20): 0.792 RDfolder: 0.556 Sensitivity CMfinder(20): 0.679 RDfolder: 0.511 Positive Predictive Value CMfinder(20): 0.927 RDfolder: 0.611 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs MCFold Matthews Correlation Coefficient CMfinder(20): 0.738 MCFold: 0.498 Sensitivity CMfinder(20): 0.608 MCFold: 0.558 Positive Predictive Value CMfinder(20): 0.898 MCFold: 0.452 Number of pairs reference - predicted secondary structure: 254 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs NanoFolder Matthews Correlation Coefficient CMfinder(20): 0.689 NanoFolder: 0.333 Sensitivity CMfinder(20): 0.554 NanoFolder: 0.387 Positive Predictive Value CMfinder(20): 0.862 NanoFolder: 0.295 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CMfinder(20) vs Mastr(seed) Matthews Correlation Coefficient CMfinder(20): 0.665 Mastr(seed): 0.270 Sensitivity CMfinder(20): 0.518 Mastr(seed): 0.090 Positive Predictive Value CMfinder(20): 0.858 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 150 Wilcoxon single-rank test P-value: 3.56938820447e-08
CRWrnafold	881 ContextFold vs CRWrnafold Matthews Correlation Coefficient ContextFold: 0.779 CRWrnafold: 0.630 Sensitivity ContextFold: 0.741 CRWrnafold: 0.618 Positive Predictive Value ContextFold: 0.823 CRWrnafold: 0.648 Number of pairs reference - predicted secondary structure: 881 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 TurboFold(20) vs CRWrnafold Matthews Correlation Coefficient TurboFold(20): 0.889 CRWrnafold: 0.783 Sensitivity TurboFold(20): 0.861 CRWrnafold: 0.771 Positive Predictive Value TurboFold(20): 0.919 CRWrnafold: 0.798 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	216 CentroidAlifold(seed) vs CRWrnafold Matthews Correlation Coefficient CentroidAlifold(seed): 0.790 CRWrnafold: 0.705 Sensitivity CentroidAlifold(seed): 0.699 CRWrnafold: 0.696 Positive Predictive Value CentroidAlifold(seed): 0.896 CRWrnafold: 0.716 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	881 CentroidHomfold‑LAST vs CRWrnafold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.736 CRWrnafold: 0.630 Sensitivity CentroidHomfold‑LAST: 0.665 CRWrnafold: 0.618 Positive Predictive Value CentroidHomfold‑LAST: 0.818 CRWrnafold: 0.648 Number of pairs reference - predicted secondary structure: 881 Wilcoxon single-rank test P-value: 3.56938820447e-08	498 PETfold_pre2.0(seed) vs CRWrnafold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.879 CRWrnafold: 0.718 Sensitivity PETfold_pre2.0(seed): 0.825 CRWrnafold: 0.713 Positive Predictive Value PETfold_pre2.0(seed): 0.938 CRWrnafold: 0.725 Number of pairs reference - predicted secondary structure: 498 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 TurboFold(seed) vs CRWrnafold Matthews Correlation Coefficient TurboFold(seed): 0.798 CRWrnafold: 0.724 Sensitivity TurboFold(seed): 0.766 CRWrnafold: 0.715 Positive Predictive Value TurboFold(seed): 0.835 CRWrnafold: 0.736 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	233 MXScarna(seed) vs CRWrnafold Matthews Correlation Coefficient MXScarna(seed): 0.750 CRWrnafold: 0.701 Sensitivity MXScarna(seed): 0.712 CRWrnafold: 0.693 Positive Predictive Value MXScarna(seed): 0.793 CRWrnafold: 0.713 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 CentroidAlifold(20) vs CRWrnafold Matthews Correlation Coefficient CentroidAlifold(20): 0.849 CRWrnafold: 0.783 Sensitivity CentroidAlifold(20): 0.754 CRWrnafold: 0.771 Positive Predictive Value CentroidAlifold(20): 0.957 CRWrnafold: 0.798 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 PETfold_pre2.0(20) vs CRWrnafold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 CRWrnafold: 0.783 Sensitivity PETfold_pre2.0(20): 0.737 CRWrnafold: 0.771 Positive Predictive Value PETfold_pre2.0(20): 0.975 CRWrnafold: 0.798 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 MXScarna(20) vs CRWrnafold Matthews Correlation Coefficient MXScarna(20): 0.838 CRWrnafold: 0.783 Sensitivity MXScarna(20): 0.791 CRWrnafold: 0.771 Positive Predictive Value MXScarna(20): 0.891 CRWrnafold: 0.798 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	314 PPfold(20) vs CRWrnafold Matthews Correlation Coefficient PPfold(20): 0.839 CRWrnafold: 0.782 Sensitivity PPfold(20): 0.721 CRWrnafold: 0.769 Positive Predictive Value PPfold(20): 0.977 CRWrnafold: 0.797 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RNAalifold(20) vs CRWrnafold Matthews Correlation Coefficient RNAalifold(20): 0.816 CRWrnafold: 0.783 Sensitivity RNAalifold(20): 0.690 CRWrnafold: 0.771 Positive Predictive Value RNAalifold(20): 0.966 CRWrnafold: 0.798 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RSpredict(20) vs CRWrnafold Matthews Correlation Coefficient RSpredict(20): 0.789 CRWrnafold: 0.783 Sensitivity RSpredict(20): 0.693 CRWrnafold: 0.771 Positive Predictive Value RSpredict(20): 0.901 CRWrnafold: 0.798 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 4.98094999346e-07	881 IPknot vs CRWrnafold Matthews Correlation Coefficient IPknot: 0.694 CRWrnafold: 0.630 Sensitivity IPknot: 0.661 CRWrnafold: 0.618 Positive Predictive Value IPknot: 0.733 CRWrnafold: 0.648 Number of pairs reference - predicted secondary structure: 881 Wilcoxon single-rank test P-value: 3.56938820447e-08	311 Multilign(20) vs CRWrnafold Matthews Correlation Coefficient Multilign(20): 0.784 CRWrnafold: 0.780 Sensitivity Multilign(20): 0.697 CRWrnafold: 0.767 Positive Predictive Value Multilign(20): 0.885 CRWrnafold: 0.795 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 0.000150377120024	881 CentroidFold vs CRWrnafold Matthews Correlation Coefficient CentroidFold: 0.645 CRWrnafold: 0.630 Sensitivity CentroidFold: 0.612 CRWrnafold: 0.618 Positive Predictive Value CentroidFold: 0.684 CRWrnafold: 0.648 Number of pairs reference - predicted secondary structure: 881 Wilcoxon single-rank test P-value: 3.56938820447e-08	881 Contrafold vs CRWrnafold Matthews Correlation Coefficient Contrafold: 0.643 CRWrnafold: 0.630 Sensitivity Contrafold: 0.634 CRWrnafold: 0.618 Positive Predictive Value Contrafold: 0.657 CRWrnafold: 0.648 Number of pairs reference - predicted secondary structure: 881 Wilcoxon single-rank test P-value: 3.85233844192e-08	315 CRWrnafold vs RNASampler(20) Matthews Correlation Coefficient CRWrnafold: 0.784 RNASampler(20): 0.770 Sensitivity CRWrnafold: 0.771 RNASampler(20): 0.622 Positive Predictive Value CRWrnafold: 0.799 RNASampler(20): 0.957 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.85233844192e-08	319 CRWrnafold vs Murlet(20) Matthews Correlation Coefficient CRWrnafold: 0.783 Murlet(20): 0.750 Sensitivity CRWrnafold: 0.771 Murlet(20): 0.619 Positive Predictive Value CRWrnafold: 0.798 Murlet(20): 0.913 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 CMfinder(seed) vs CRWrnafold Matthews Correlation Coefficient CMfinder(seed): 0.571 CRWrnafold: 0.445 Sensitivity CMfinder(seed): 0.439 CRWrnafold: 0.424 Positive Predictive Value CMfinder(seed): 0.747 CRWrnafold: 0.474 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	881 MaxExpect vs CRWrnafold Matthews Correlation Coefficient MaxExpect: 0.633 CRWrnafold: 0.630 Sensitivity MaxExpect: 0.617 CRWrnafold: 0.618 Positive Predictive Value MaxExpect: 0.654 CRWrnafold: 0.648 Number of pairs reference - predicted secondary structure: 881 Wilcoxon single-rank test P-value: 3.90487810335e-05	316 CRWrnafold vs CMfinder(20) Matthews Correlation Coefficient CRWrnafold: 0.781 CMfinder(20): 0.735 Sensitivity CRWrnafold: 0.769 CMfinder(20): 0.603 Positive Predictive Value CRWrnafold: 0.796 CMfinder(20): 0.899 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08		= CRWrnafold vs ProbKnot Matthews Correlation Coefficient CRWrnafold: 0.630 ProbKnot: 0.630 Sensitivity CRWrnafold: 0.618 ProbKnot: 0.622 Positive Predictive Value CRWrnafold: 0.648 ProbKnot: 0.644 Number of pairs reference - predicted secondary structure: 881 Wilcoxon single-rank test P-value: 0.893076023681	+ CRWrnafold vs Mastr(20) Matthews Correlation Coefficient CRWrnafold: 0.783 Mastr(20): 0.708 Sensitivity CRWrnafold: 0.771 Mastr(20): 0.635 Positive Predictive Value CRWrnafold: 0.798 Mastr(20): 0.793 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs Fold Matthews Correlation Coefficient CRWrnafold: 0.630 Fold: 0.628 Sensitivity CRWrnafold: 0.618 Fold: 0.620 Positive Predictive Value CRWrnafold: 0.648 Fold: 0.641 Number of pairs reference - predicted secondary structure: 881 Wilcoxon single-rank test P-value: 0.00094449411354	+ CRWrnafold vs UNAFold Matthews Correlation Coefficient CRWrnafold: 0.630 UNAFold: 0.619 Sensitivity CRWrnafold: 0.618 UNAFold: 0.605 Positive Predictive Value CRWrnafold: 0.648 UNAFold: 0.639 Number of pairs reference - predicted secondary structure: 881 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs PknotsRG Matthews Correlation Coefficient CRWrnafold: 0.630 PknotsRG: 0.617 Sensitivity CRWrnafold: 0.618 PknotsRG: 0.610 Positive Predictive Value CRWrnafold: 0.648 PknotsRG: 0.630 Number of pairs reference - predicted secondary structure: 881 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs Sfold Matthews Correlation Coefficient CRWrnafold: 0.630 Sfold: 0.618 Sensitivity CRWrnafold: 0.618 Sfold: 0.581 Positive Predictive Value CRWrnafold: 0.648 Sfold: 0.663 Number of pairs reference - predicted secondary structure: 881 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs RNAalifold(seed) Matthews Correlation Coefficient CRWrnafold: 0.711 RNAalifold(seed): 0.610 Sensitivity CRWrnafold: 0.701 RNAalifold(seed): 0.404 Positive Predictive Value CRWrnafold: 0.724 RNAalifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs RNAsubopt Matthews Correlation Coefficient CRWrnafold: 0.630 RNAsubopt: 0.615 Sensitivity CRWrnafold: 0.618 RNAsubopt: 0.609 Positive Predictive Value CRWrnafold: 0.648 RNAsubopt: 0.626 Number of pairs reference - predicted secondary structure: 881 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs HotKnots Matthews Correlation Coefficient CRWrnafold: 0.632 HotKnots: 0.613 Sensitivity CRWrnafold: 0.620 HotKnots: 0.607 Positive Predictive Value CRWrnafold: 0.650 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 874 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs RNAfold Matthews Correlation Coefficient CRWrnafold: 0.630 RNAfold: 0.612 Sensitivity CRWrnafold: 0.618 RNAfold: 0.603 Positive Predictive Value CRWrnafold: 0.648 RNAfold: 0.625 Number of pairs reference - predicted secondary structure: 881 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs RNAshapes Matthews Correlation Coefficient CRWrnafold: 0.630 RNAshapes: 0.612 Sensitivity CRWrnafold: 0.618 RNAshapes: 0.602 Positive Predictive Value CRWrnafold: 0.648 RNAshapes: 0.627 Number of pairs reference - predicted secondary structure: 881 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASampler(seed) vs CRWrnafold Matthews Correlation Coefficient RNASampler(seed): 0.557 CRWrnafold: 0.473 Sensitivity RNASampler(seed): 0.389 CRWrnafold: 0.451 Positive Predictive Value RNASampler(seed): 0.802 CRWrnafold: 0.501 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs Afold Matthews Correlation Coefficient CRWrnafold: 0.607 Afold: 0.558 Sensitivity CRWrnafold: 0.583 Afold: 0.541 Positive Predictive Value CRWrnafold: 0.637 Afold: 0.581 Number of pairs reference - predicted secondary structure: 529 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs Pknots Matthews Correlation Coefficient CRWrnafold: 0.614 Pknots: 0.606 Sensitivity CRWrnafold: 0.600 Pknots: 0.595 Positive Predictive Value CRWrnafold: 0.634 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 696 Wilcoxon single-rank test P-value: 5.62644058675e-08	+ CRWrnafold vs McQFold Matthews Correlation Coefficient CRWrnafold: 0.630 McQFold: 0.583 Sensitivity CRWrnafold: 0.618 McQFold: 0.557 Positive Predictive Value CRWrnafold: 0.648 McQFold: 0.616 Number of pairs reference - predicted secondary structure: 881 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs Carnac(20) Matthews Correlation Coefficient CRWrnafold: 0.783 Carnac(20): 0.675 Sensitivity CRWrnafold: 0.771 Carnac(20): 0.500 Positive Predictive Value CRWrnafold: 0.798 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs RNASLOpt Matthews Correlation Coefficient CRWrnafold: 0.630 RNASLOpt: 0.562 Sensitivity CRWrnafold: 0.618 RNASLOpt: 0.521 Positive Predictive Value CRWrnafold: 0.648 RNASLOpt: 0.613 Number of pairs reference - predicted secondary structure: 881 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs Cylofold Matthews Correlation Coefficient CRWrnafold: 0.667 Cylofold: 0.577 Sensitivity CRWrnafold: 0.651 Cylofold: 0.553 Positive Predictive Value CRWrnafold: 0.688 Cylofold: 0.608 Number of pairs reference - predicted secondary structure: 795 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Multilign(seed) vs CRWrnafold Matthews Correlation Coefficient Multilign(seed): 0.485 CRWrnafold: 0.415 Sensitivity Multilign(seed): 0.386 CRWrnafold: 0.395 Positive Predictive Value Multilign(seed): 0.619 CRWrnafold: 0.447 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.04409141234e-08	+ CRWrnafold vs RNAwolf Matthews Correlation Coefficient CRWrnafold: 0.630 RNAwolf: 0.518 Sensitivity CRWrnafold: 0.618 RNAwolf: 0.523 Positive Predictive Value CRWrnafold: 0.648 RNAwolf: 0.520 Number of pairs reference - predicted secondary structure: 881 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs PPfold(seed) Matthews Correlation Coefficient CRWrnafold: 0.702 PPfold(seed): 0.380 Sensitivity CRWrnafold: 0.702 PPfold(seed): 0.170 Positive Predictive Value CRWrnafold: 0.706 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs Murlet(seed) Matthews Correlation Coefficient CRWrnafold: 0.516 Murlet(seed): 0.468 Sensitivity CRWrnafold: 0.496 Murlet(seed): 0.266 Positive Predictive Value CRWrnafold: 0.543 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs Alterna Matthews Correlation Coefficient CRWrnafold: 0.615 Alterna: 0.552 Sensitivity CRWrnafold: 0.601 Alterna: 0.546 Positive Predictive Value CRWrnafold: 0.635 Alterna: 0.565 Number of pairs reference - predicted secondary structure: 692 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs Carnac(seed) Matthews Correlation Coefficient CRWrnafold: 0.599 Carnac(seed): 0.415 Sensitivity CRWrnafold: 0.584 Carnac(seed): 0.196 Positive Predictive Value CRWrnafold: 0.618 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs Vsfold4 Matthews Correlation Coefficient CRWrnafold: 0.630 Vsfold4: 0.487 Sensitivity CRWrnafold: 0.618 Vsfold4: 0.447 Positive Predictive Value CRWrnafold: 0.648 Vsfold4: 0.537 Number of pairs reference - predicted secondary structure: 881 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs RSpredict(seed) Matthews Correlation Coefficient CRWrnafold: 0.705 RSpredict(seed): 0.373 Sensitivity CRWrnafold: 0.696 RSpredict(seed): 0.251 Positive Predictive Value CRWrnafold: 0.716 RSpredict(seed): 0.562 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs Vsfold5 Matthews Correlation Coefficient CRWrnafold: 0.630 Vsfold5: 0.477 Sensitivity CRWrnafold: 0.618 Vsfold5: 0.451 Positive Predictive Value CRWrnafold: 0.648 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 881 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs RDfolder Matthews Correlation Coefficient CRWrnafold: 0.615 RDfolder: 0.520 Sensitivity CRWrnafold: 0.601 RDfolder: 0.464 Positive Predictive Value CRWrnafold: 0.635 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 692 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs MCFold Matthews Correlation Coefficient CRWrnafold: 0.629 MCFold: 0.473 Sensitivity CRWrnafold: 0.614 MCFold: 0.524 Positive Predictive Value CRWrnafold: 0.649 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 760 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs NanoFolder Matthews Correlation Coefficient CRWrnafold: 0.671 NanoFolder: 0.335 Sensitivity CRWrnafold: 0.654 NanoFolder: 0.384 Positive Predictive Value CRWrnafold: 0.692 NanoFolder: 0.301 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ CRWrnafold vs Mastr(seed) Matthews Correlation Coefficient CRWrnafold: 0.702 Mastr(seed): 0.263 Sensitivity CRWrnafold: 0.694 Mastr(seed): 0.089 Positive Predictive Value CRWrnafold: 0.714 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08
ProbKnot	882 ContextFold vs ProbKnot Matthews Correlation Coefficient ContextFold: 0.779 ProbKnot: 0.630 Sensitivity ContextFold: 0.741 ProbKnot: 0.622 Positive Predictive Value ContextFold: 0.823 ProbKnot: 0.644 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 TurboFold(20) vs ProbKnot Matthews Correlation Coefficient TurboFold(20): 0.889 ProbKnot: 0.707 Sensitivity TurboFold(20): 0.861 ProbKnot: 0.702 Positive Predictive Value TurboFold(20): 0.919 ProbKnot: 0.716 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	216 CentroidAlifold(seed) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(seed): 0.790 ProbKnot: 0.687 Sensitivity CentroidAlifold(seed): 0.699 ProbKnot: 0.680 Positive Predictive Value CentroidAlifold(seed): 0.896 ProbKnot: 0.697 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 CentroidHomfold‑LAST vs ProbKnot Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.736 ProbKnot: 0.630 Sensitivity CentroidHomfold‑LAST: 0.665 ProbKnot: 0.622 Positive Predictive Value CentroidHomfold‑LAST: 0.818 ProbKnot: 0.644 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	498 PETfold_pre2.0(seed) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.879 ProbKnot: 0.690 Sensitivity PETfold_pre2.0(seed): 0.825 ProbKnot: 0.692 Positive Predictive Value PETfold_pre2.0(seed): 0.938 ProbKnot: 0.692 Number of pairs reference - predicted secondary structure: 498 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 TurboFold(seed) vs ProbKnot Matthews Correlation Coefficient TurboFold(seed): 0.798 ProbKnot: 0.750 Sensitivity TurboFold(seed): 0.766 ProbKnot: 0.735 Positive Predictive Value TurboFold(seed): 0.835 ProbKnot: 0.769 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 5.23657817852e-08	233 MXScarna(seed) vs ProbKnot Matthews Correlation Coefficient MXScarna(seed): 0.750 ProbKnot: 0.684 Sensitivity MXScarna(seed): 0.712 ProbKnot: 0.678 Positive Predictive Value MXScarna(seed): 0.793 ProbKnot: 0.694 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 CentroidAlifold(20) vs ProbKnot Matthews Correlation Coefficient CentroidAlifold(20): 0.849 ProbKnot: 0.707 Sensitivity CentroidAlifold(20): 0.754 ProbKnot: 0.702 Positive Predictive Value CentroidAlifold(20): 0.957 ProbKnot: 0.716 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 PETfold_pre2.0(20) vs ProbKnot Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 ProbKnot: 0.707 Sensitivity PETfold_pre2.0(20): 0.737 ProbKnot: 0.702 Positive Predictive Value PETfold_pre2.0(20): 0.975 ProbKnot: 0.716 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 MXScarna(20) vs ProbKnot Matthews Correlation Coefficient MXScarna(20): 0.838 ProbKnot: 0.707 Sensitivity MXScarna(20): 0.791 ProbKnot: 0.702 Positive Predictive Value MXScarna(20): 0.891 ProbKnot: 0.716 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	314 PPfold(20) vs ProbKnot Matthews Correlation Coefficient PPfold(20): 0.839 ProbKnot: 0.704 Sensitivity PPfold(20): 0.721 ProbKnot: 0.699 Positive Predictive Value PPfold(20): 0.977 ProbKnot: 0.713 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RNAalifold(20) vs ProbKnot Matthews Correlation Coefficient RNAalifold(20): 0.816 ProbKnot: 0.707 Sensitivity RNAalifold(20): 0.690 ProbKnot: 0.702 Positive Predictive Value RNAalifold(20): 0.966 ProbKnot: 0.716 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RSpredict(20) vs ProbKnot Matthews Correlation Coefficient RSpredict(20): 0.789 ProbKnot: 0.707 Sensitivity RSpredict(20): 0.693 ProbKnot: 0.702 Positive Predictive Value RSpredict(20): 0.901 ProbKnot: 0.716 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 IPknot vs ProbKnot Matthews Correlation Coefficient IPknot: 0.694 ProbKnot: 0.630 Sensitivity IPknot: 0.661 ProbKnot: 0.622 Positive Predictive Value IPknot: 0.733 ProbKnot: 0.644 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	311 Multilign(20) vs ProbKnot Matthews Correlation Coefficient Multilign(20): 0.784 ProbKnot: 0.706 Sensitivity Multilign(20): 0.697 ProbKnot: 0.701 Positive Predictive Value Multilign(20): 0.885 ProbKnot: 0.715 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 CentroidFold vs ProbKnot Matthews Correlation Coefficient CentroidFold: 0.645 ProbKnot: 0.630 Sensitivity CentroidFold: 0.612 ProbKnot: 0.622 Positive Predictive Value CentroidFold: 0.684 ProbKnot: 0.644 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 Contrafold vs ProbKnot Matthews Correlation Coefficient Contrafold: 0.643 ProbKnot: 0.630 Sensitivity Contrafold: 0.634 ProbKnot: 0.622 Positive Predictive Value Contrafold: 0.657 ProbKnot: 0.644 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	315 RNASampler(20) vs ProbKnot Matthews Correlation Coefficient RNASampler(20): 0.770 ProbKnot: 0.709 Sensitivity RNASampler(20): 0.622 ProbKnot: 0.704 Positive Predictive Value RNASampler(20): 0.957 ProbKnot: 0.718 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	319 Murlet(20) vs ProbKnot Matthews Correlation Coefficient Murlet(20): 0.750 ProbKnot: 0.707 Sensitivity Murlet(20): 0.619 ProbKnot: 0.703 Positive Predictive Value Murlet(20): 0.913 ProbKnot: 0.716 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 CMfinder(seed) vs ProbKnot Matthews Correlation Coefficient CMfinder(seed): 0.571 ProbKnot: 0.564 Sensitivity CMfinder(seed): 0.439 ProbKnot: 0.536 Positive Predictive Value CMfinder(seed): 0.747 ProbKnot: 0.599 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 0.0139030957526	882 MaxExpect vs ProbKnot Matthews Correlation Coefficient MaxExpect: 0.633 ProbKnot: 0.630 Sensitivity MaxExpect: 0.617 ProbKnot: 0.622 Positive Predictive Value MaxExpect: 0.654 ProbKnot: 0.644 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	316 CMfinder(20) vs ProbKnot Matthews Correlation Coefficient CMfinder(20): 0.735 ProbKnot: 0.706 Sensitivity CMfinder(20): 0.603 ProbKnot: 0.702 Positive Predictive Value CMfinder(20): 0.899 ProbKnot: 0.715 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	881 CRWrnafold vs ProbKnot Matthews Correlation Coefficient CRWrnafold: 0.630 ProbKnot: 0.630 Sensitivity CRWrnafold: 0.618 ProbKnot: 0.622 Positive Predictive Value CRWrnafold: 0.648 ProbKnot: 0.644 Number of pairs reference - predicted secondary structure: 881 Wilcoxon single-rank test P-value: 0.893076023681		= Mastr(20) vs ProbKnot Matthews Correlation Coefficient Mastr(20): 0.708 ProbKnot: 0.707 Sensitivity Mastr(20): 0.635 ProbKnot: 0.702 Positive Predictive Value Mastr(20): 0.793 ProbKnot: 0.716 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 0.27038065226	+ ProbKnot vs Fold Matthews Correlation Coefficient ProbKnot: 0.630 Fold: 0.628 Sensitivity ProbKnot: 0.622 Fold: 0.620 Positive Predictive Value ProbKnot: 0.644 Fold: 0.641 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 1.27481660653e-07	+ ProbKnot vs UNAFold Matthews Correlation Coefficient ProbKnot: 0.630 UNAFold: 0.620 Sensitivity ProbKnot: 0.622 UNAFold: 0.605 Positive Predictive Value ProbKnot: 0.644 UNAFold: 0.639 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs PknotsRG Matthews Correlation Coefficient ProbKnot: 0.630 PknotsRG: 0.617 Sensitivity ProbKnot: 0.622 PknotsRG: 0.610 Positive Predictive Value ProbKnot: 0.644 PknotsRG: 0.630 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Sfold Matthews Correlation Coefficient ProbKnot: 0.630 Sfold: 0.618 Sensitivity ProbKnot: 0.622 Sfold: 0.581 Positive Predictive Value ProbKnot: 0.644 Sfold: 0.663 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RNAalifold(seed) Matthews Correlation Coefficient ProbKnot: 0.689 RNAalifold(seed): 0.610 Sensitivity ProbKnot: 0.680 RNAalifold(seed): 0.404 Positive Predictive Value ProbKnot: 0.701 RNAalifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RNAsubopt Matthews Correlation Coefficient ProbKnot: 0.630 RNAsubopt: 0.615 Sensitivity ProbKnot: 0.622 RNAsubopt: 0.609 Positive Predictive Value ProbKnot: 0.644 RNAsubopt: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs HotKnots Matthews Correlation Coefficient ProbKnot: 0.632 HotKnots: 0.613 Sensitivity ProbKnot: 0.623 HotKnots: 0.607 Positive Predictive Value ProbKnot: 0.646 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 875 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RNAfold Matthews Correlation Coefficient ProbKnot: 0.630 RNAfold: 0.612 Sensitivity ProbKnot: 0.622 RNAfold: 0.604 Positive Predictive Value ProbKnot: 0.644 RNAfold: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RNAshapes Matthews Correlation Coefficient ProbKnot: 0.630 RNAshapes: 0.612 Sensitivity ProbKnot: 0.622 RNAshapes: 0.602 Positive Predictive Value ProbKnot: 0.644 RNAshapes: 0.628 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RNASampler(seed) Matthews Correlation Coefficient ProbKnot: 0.582 RNASampler(seed): 0.557 Sensitivity ProbKnot: 0.554 RNASampler(seed): 0.389 Positive Predictive Value ProbKnot: 0.615 RNASampler(seed): 0.802 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Afold Matthews Correlation Coefficient ProbKnot: 0.616 Afold: 0.558 Sensitivity ProbKnot: 0.594 Afold: 0.541 Positive Predictive Value ProbKnot: 0.645 Afold: 0.582 Number of pairs reference - predicted secondary structure: 530 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Pknots Matthews Correlation Coefficient ProbKnot: 0.639 Pknots: 0.606 Sensitivity ProbKnot: 0.631 Pknots: 0.595 Positive Predictive Value ProbKnot: 0.655 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs McQFold Matthews Correlation Coefficient ProbKnot: 0.630 McQFold: 0.583 Sensitivity ProbKnot: 0.622 McQFold: 0.557 Positive Predictive Value ProbKnot: 0.644 McQFold: 0.616 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Carnac(20) Matthews Correlation Coefficient ProbKnot: 0.707 Carnac(20): 0.675 Sensitivity ProbKnot: 0.702 Carnac(20): 0.500 Positive Predictive Value ProbKnot: 0.716 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RNASLOpt Matthews Correlation Coefficient ProbKnot: 0.630 RNASLOpt: 0.562 Sensitivity ProbKnot: 0.622 RNASLOpt: 0.521 Positive Predictive Value ProbKnot: 0.644 RNASLOpt: 0.613 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Cylofold Matthews Correlation Coefficient ProbKnot: 0.658 Cylofold: 0.577 Sensitivity ProbKnot: 0.649 Cylofold: 0.554 Positive Predictive Value ProbKnot: 0.673 Cylofold: 0.608 Number of pairs reference - predicted secondary structure: 796 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Multilign(seed) Matthews Correlation Coefficient ProbKnot: 0.505 Multilign(seed): 0.485 Sensitivity ProbKnot: 0.479 Multilign(seed): 0.386 Positive Predictive Value ProbKnot: 0.542 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.23248012054e-07	+ ProbKnot vs RNAwolf Matthews Correlation Coefficient ProbKnot: 0.630 RNAwolf: 0.518 Sensitivity ProbKnot: 0.622 RNAwolf: 0.523 Positive Predictive Value ProbKnot: 0.644 RNAwolf: 0.520 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs PPfold(seed) Matthews Correlation Coefficient ProbKnot: 0.726 PPfold(seed): 0.380 Sensitivity ProbKnot: 0.722 PPfold(seed): 0.170 Positive Predictive Value ProbKnot: 0.733 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Murlet(seed) Matthews Correlation Coefficient ProbKnot: 0.615 Murlet(seed): 0.468 Sensitivity ProbKnot: 0.591 Murlet(seed): 0.266 Positive Predictive Value ProbKnot: 0.646 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Alterna Matthews Correlation Coefficient ProbKnot: 0.640 Alterna: 0.552 Sensitivity ProbKnot: 0.632 Alterna: 0.547 Positive Predictive Value ProbKnot: 0.656 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Carnac(seed) Matthews Correlation Coefficient ProbKnot: 0.651 Carnac(seed): 0.415 Sensitivity ProbKnot: 0.636 Carnac(seed): 0.196 Positive Predictive Value ProbKnot: 0.671 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Vsfold4 Matthews Correlation Coefficient ProbKnot: 0.630 Vsfold4: 0.487 Sensitivity ProbKnot: 0.622 Vsfold4: 0.447 Positive Predictive Value ProbKnot: 0.644 Vsfold4: 0.537 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RSpredict(seed) Matthews Correlation Coefficient ProbKnot: 0.687 RSpredict(seed): 0.373 Sensitivity ProbKnot: 0.680 RSpredict(seed): 0.251 Positive Predictive Value ProbKnot: 0.697 RSpredict(seed): 0.562 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Vsfold5 Matthews Correlation Coefficient ProbKnot: 0.630 Vsfold5: 0.477 Sensitivity ProbKnot: 0.622 Vsfold5: 0.450 Positive Predictive Value ProbKnot: 0.644 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs RDfolder Matthews Correlation Coefficient ProbKnot: 0.640 RDfolder: 0.520 Sensitivity ProbKnot: 0.632 RDfolder: 0.464 Positive Predictive Value ProbKnot: 0.656 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs MCFold Matthews Correlation Coefficient ProbKnot: 0.639 MCFold: 0.473 Sensitivity ProbKnot: 0.628 MCFold: 0.524 Positive Predictive Value ProbKnot: 0.656 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs NanoFolder Matthews Correlation Coefficient ProbKnot: 0.671 NanoFolder: 0.335 Sensitivity ProbKnot: 0.658 NanoFolder: 0.384 Positive Predictive Value ProbKnot: 0.688 NanoFolder: 0.301 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ ProbKnot vs Mastr(seed) Matthews Correlation Coefficient ProbKnot: 0.684 Mastr(seed): 0.263 Sensitivity ProbKnot: 0.678 Mastr(seed): 0.089 Positive Predictive Value ProbKnot: 0.694 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08
Mastr(20)	320 ContextFold vs Mastr(20) Matthews Correlation Coefficient ContextFold: 0.923 Mastr(20): 0.708 Sensitivity ContextFold: 0.898 Mastr(20): 0.635 Positive Predictive Value ContextFold: 0.949 Mastr(20): 0.793 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 TurboFold(20) vs Mastr(20) Matthews Correlation Coefficient TurboFold(20): 0.889 Mastr(20): 0.708 Sensitivity TurboFold(20): 0.861 Mastr(20): 0.635 Positive Predictive Value TurboFold(20): 0.919 Mastr(20): 0.793 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	141 CentroidAlifold(seed) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.815 Mastr(20): 0.659 Sensitivity CentroidAlifold(seed): 0.743 Mastr(20): 0.520 Positive Predictive Value CentroidAlifold(seed): 0.897 Mastr(20): 0.839 Number of pairs reference - predicted secondary structure: 141 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 CentroidHomfold‑LAST vs Mastr(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.858 Mastr(20): 0.708 Sensitivity CentroidHomfold‑LAST: 0.821 Mastr(20): 0.635 Positive Predictive Value CentroidHomfold‑LAST: 0.900 Mastr(20): 0.793 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	319 PETfold_pre2.0(seed) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.885 Mastr(20): 0.710 Sensitivity PETfold_pre2.0(seed): 0.832 Mastr(20): 0.638 Positive Predictive Value PETfold_pre2.0(seed): 0.944 Mastr(20): 0.793 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 TurboFold(seed) vs Mastr(20) Matthews Correlation Coefficient TurboFold(seed): 0.880 Mastr(20): 0.720 Sensitivity TurboFold(seed): 0.875 Mastr(20): 0.559 Positive Predictive Value TurboFold(seed): 0.886 Mastr(20): 0.931 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 9.54892753461e-09	153 MXScarna(seed) vs Mastr(20) Matthews Correlation Coefficient MXScarna(seed): 0.792 Mastr(20): 0.678 Sensitivity MXScarna(seed): 0.756 Mastr(20): 0.547 Positive Predictive Value MXScarna(seed): 0.832 Mastr(20): 0.843 Number of pairs reference - predicted secondary structure: 153 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 CentroidAlifold(20) vs Mastr(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.849 Mastr(20): 0.708 Sensitivity CentroidAlifold(20): 0.754 Mastr(20): 0.635 Positive Predictive Value CentroidAlifold(20): 0.957 Mastr(20): 0.793 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 PETfold_pre2.0(20) vs Mastr(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 Mastr(20): 0.708 Sensitivity PETfold_pre2.0(20): 0.737 Mastr(20): 0.635 Positive Predictive Value PETfold_pre2.0(20): 0.975 Mastr(20): 0.793 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 MXScarna(20) vs Mastr(20) Matthews Correlation Coefficient MXScarna(20): 0.838 Mastr(20): 0.708 Sensitivity MXScarna(20): 0.791 Mastr(20): 0.635 Positive Predictive Value MXScarna(20): 0.891 Mastr(20): 0.793 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	314 PPfold(20) vs Mastr(20) Matthews Correlation Coefficient PPfold(20): 0.839 Mastr(20): 0.714 Sensitivity PPfold(20): 0.721 Mastr(20): 0.644 Positive Predictive Value PPfold(20): 0.977 Mastr(20): 0.796 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RNAalifold(20) vs Mastr(20) Matthews Correlation Coefficient RNAalifold(20): 0.816 Mastr(20): 0.708 Sensitivity RNAalifold(20): 0.690 Mastr(20): 0.635 Positive Predictive Value RNAalifold(20): 0.966 Mastr(20): 0.793 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RSpredict(20) vs Mastr(20) Matthews Correlation Coefficient RSpredict(20): 0.789 Mastr(20): 0.708 Sensitivity RSpredict(20): 0.693 Mastr(20): 0.635 Positive Predictive Value RSpredict(20): 0.901 Mastr(20): 0.793 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 IPknot vs Mastr(20) Matthews Correlation Coefficient IPknot: 0.783 Mastr(20): 0.708 Sensitivity IPknot: 0.761 Mastr(20): 0.635 Positive Predictive Value IPknot: 0.807 Mastr(20): 0.793 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	311 Multilign(20) vs Mastr(20) Matthews Correlation Coefficient Multilign(20): 0.784 Mastr(20): 0.712 Sensitivity Multilign(20): 0.697 Mastr(20): 0.644 Positive Predictive Value Multilign(20): 0.885 Mastr(20): 0.792 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 CentroidFold vs Mastr(20) Matthews Correlation Coefficient CentroidFold: 0.735 Mastr(20): 0.708 Sensitivity CentroidFold: 0.710 Mastr(20): 0.635 Positive Predictive Value CentroidFold: 0.764 Mastr(20): 0.793 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.85233844192e-08	320 Contrafold vs Mastr(20) Matthews Correlation Coefficient Contrafold: 0.733 Mastr(20): 0.708 Sensitivity Contrafold: 0.729 Mastr(20): 0.635 Positive Predictive Value Contrafold: 0.740 Mastr(20): 0.793 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	315 RNASampler(20) vs Mastr(20) Matthews Correlation Coefficient RNASampler(20): 0.770 Mastr(20): 0.710 Sensitivity RNASampler(20): 0.622 Mastr(20): 0.639 Positive Predictive Value RNASampler(20): 0.957 Mastr(20): 0.793 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	319 Murlet(20) vs Mastr(20) Matthews Correlation Coefficient Murlet(20): 0.750 Mastr(20): 0.710 Sensitivity Murlet(20): 0.619 Mastr(20): 0.638 Positive Predictive Value Murlet(20): 0.913 Mastr(20): 0.793 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 Mastr(20) vs CMfinder(seed) Matthews Correlation Coefficient Mastr(20): 0.748 CMfinder(seed): 0.736 Sensitivity Mastr(20): 0.683 CMfinder(seed): 0.607 Positive Predictive Value Mastr(20): 0.824 CMfinder(seed): 0.898 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 1.35806673514e-06	320 MaxExpect vs Mastr(20) Matthews Correlation Coefficient MaxExpect: 0.711 Mastr(20): 0.708 Sensitivity MaxExpect: 0.701 Mastr(20): 0.635 Positive Predictive Value MaxExpect: 0.725 Mastr(20): 0.793 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 0.0256642192469	316 CMfinder(20) vs Mastr(20) Matthews Correlation Coefficient CMfinder(20): 0.735 Mastr(20): 0.712 Sensitivity CMfinder(20): 0.603 Mastr(20): 0.643 Positive Predictive Value CMfinder(20): 0.899 Mastr(20): 0.792 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 CRWrnafold vs Mastr(20) Matthews Correlation Coefficient CRWrnafold: 0.783 Mastr(20): 0.708 Sensitivity CRWrnafold: 0.771 Mastr(20): 0.635 Positive Predictive Value CRWrnafold: 0.798 Mastr(20): 0.793 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 Mastr(20) vs ProbKnot Matthews Correlation Coefficient Mastr(20): 0.708 ProbKnot: 0.707 Sensitivity Mastr(20): 0.635 ProbKnot: 0.702 Positive Predictive Value Mastr(20): 0.793 ProbKnot: 0.716 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 0.27038065226		= Fold vs Mastr(20) Matthews Correlation Coefficient Fold: 0.712 Mastr(20): 0.708 Sensitivity Fold: 0.710 Mastr(20): 0.635 Positive Predictive Value Fold: 0.717 Mastr(20): 0.793 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 0.00778217989366	= Mastr(20) vs UNAFold Matthews Correlation Coefficient Mastr(20): 0.708 UNAFold: 0.708 Sensitivity Mastr(20): 0.635 UNAFold: 0.696 Positive Predictive Value Mastr(20): 0.793 UNAFold: 0.723 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 0.600132072507	+ Mastr(20) vs PknotsRG Matthews Correlation Coefficient Mastr(20): 0.708 PknotsRG: 0.691 Sensitivity Mastr(20): 0.635 PknotsRG: 0.687 Positive Predictive Value Mastr(20): 0.793 PknotsRG: 0.699 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Mastr(20) vs Sfold Matthews Correlation Coefficient Mastr(20): 0.708 Sfold: 0.698 Sensitivity Mastr(20): 0.635 Sfold: 0.662 Positive Predictive Value Mastr(20): 0.793 Sfold: 0.740 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 5.21776328505e-08	+ Mastr(20) vs RNAalifold(seed) Matthews Correlation Coefficient Mastr(20): 0.650 RNAalifold(seed): 0.604 Sensitivity Mastr(20): 0.509 RNAalifold(seed): 0.383 Positive Predictive Value Mastr(20): 0.834 RNAalifold(seed): 0.956 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Mastr(20) vs RNAsubopt Matthews Correlation Coefficient Mastr(20): 0.708 RNAsubopt: 0.694 Sensitivity Mastr(20): 0.635 RNAsubopt: 0.693 Positive Predictive Value Mastr(20): 0.793 RNAsubopt: 0.700 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 4.48494289621e-08	+ Mastr(20) vs HotKnots Matthews Correlation Coefficient Mastr(20): 0.708 HotKnots: 0.698 Sensitivity Mastr(20): 0.635 HotKnots: 0.695 Positive Predictive Value Mastr(20): 0.793 HotKnots: 0.705 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 4.48494289621e-08	+ Mastr(20) vs RNAfold Matthews Correlation Coefficient Mastr(20): 0.708 RNAfold: 0.686 Sensitivity Mastr(20): 0.635 RNAfold: 0.681 Positive Predictive Value Mastr(20): 0.793 RNAfold: 0.695 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Mastr(20) vs RNAshapes Matthews Correlation Coefficient Mastr(20): 0.708 RNAshapes: 0.693 Sensitivity Mastr(20): 0.635 RNAshapes: 0.687 Positive Predictive Value Mastr(20): 0.793 RNAshapes: 0.702 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ Mastr(20) vs RNASampler(seed) Matthews Correlation Coefficient Mastr(20): 0.773 RNASampler(seed): 0.571 Sensitivity Mastr(20): 0.712 RNASampler(seed): 0.343 Positive Predictive Value Mastr(20): 0.843 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Mastr(20) vs Afold Matthews Correlation Coefficient Mastr(20): 0.688 Afold: 0.643 Sensitivity Mastr(20): 0.602 Afold: 0.632 Positive Predictive Value Mastr(20): 0.789 Afold: 0.659 Number of pairs reference - predicted secondary structure: 163 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Mastr(20) vs Pknots Matthews Correlation Coefficient Mastr(20): 0.727 Pknots: 0.655 Sensitivity Mastr(20): 0.672 Pknots: 0.662 Positive Predictive Value Mastr(20): 0.790 Pknots: 0.653 Number of pairs reference - predicted secondary structure: 212 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Mastr(20) vs McQFold Matthews Correlation Coefficient Mastr(20): 0.708 McQFold: 0.610 Sensitivity Mastr(20): 0.635 McQFold: 0.587 Positive Predictive Value Mastr(20): 0.793 McQFold: 0.639 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Mastr(20) vs Carnac(20) Matthews Correlation Coefficient Mastr(20): 0.708 Carnac(20): 0.675 Sensitivity Mastr(20): 0.635 Carnac(20): 0.500 Positive Predictive Value Mastr(20): 0.793 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Mastr(20) vs RNASLOpt Matthews Correlation Coefficient Mastr(20): 0.708 RNASLOpt: 0.638 Sensitivity Mastr(20): 0.635 RNASLOpt: 0.594 Positive Predictive Value Mastr(20): 0.793 RNASLOpt: 0.690 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Mastr(20) vs Cylofold Matthews Correlation Coefficient Mastr(20): 0.713 Cylofold: 0.557 Sensitivity Mastr(20): 0.641 Cylofold: 0.543 Positive Predictive Value Mastr(20): 0.796 Cylofold: 0.577 Number of pairs reference - predicted secondary structure: 304 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Mastr(20) vs Multilign(seed) Matthews Correlation Coefficient Mastr(20): 0.775 Multilign(seed): 0.334 Sensitivity Mastr(20): 0.721 Multilign(seed): 0.186 Positive Predictive Value Mastr(20): 0.838 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ Mastr(20) vs RNAwolf Matthews Correlation Coefficient Mastr(20): 0.708 RNAwolf: 0.561 Sensitivity Mastr(20): 0.635 RNAwolf: 0.565 Positive Predictive Value Mastr(20): 0.793 RNAwolf: 0.561 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Mastr(20) vs PPfold(seed) Matthews Correlation Coefficient Mastr(20): 0.719 PPfold(seed): 0.344 Sensitivity Mastr(20): 0.576 PPfold(seed): 0.128 Positive Predictive Value Mastr(20): 0.902 PPfold(seed): 0.927 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ Mastr(20) vs Murlet(seed) Matthews Correlation Coefficient Mastr(20): 0.743 Murlet(seed): 0.636 Sensitivity Mastr(20): 0.664 Murlet(seed): 0.428 Positive Predictive Value Mastr(20): 0.837 Murlet(seed): 0.952 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Mastr(20) vs Alterna Matthews Correlation Coefficient Mastr(20): 0.730 Alterna: 0.618 Sensitivity Mastr(20): 0.677 Alterna: 0.626 Positive Predictive Value Mastr(20): 0.790 Alterna: 0.616 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Mastr(20) vs Carnac(seed) Matthews Correlation Coefficient Mastr(20): 0.741 Carnac(seed): 0.431 Sensitivity Mastr(20): 0.633 Carnac(seed): 0.206 Positive Predictive Value Mastr(20): 0.870 Carnac(seed): 0.907 Number of pairs reference - predicted secondary structure: 68 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Mastr(20) vs Vsfold4 Matthews Correlation Coefficient Mastr(20): 0.708 Vsfold4: 0.502 Sensitivity Mastr(20): 0.635 Vsfold4: 0.466 Positive Predictive Value Mastr(20): 0.793 Vsfold4: 0.546 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Mastr(20) vs RSpredict(seed) Matthews Correlation Coefficient Mastr(20): 0.659 RSpredict(seed): 0.414 Sensitivity Mastr(20): 0.520 RSpredict(seed): 0.279 Positive Predictive Value Mastr(20): 0.839 RSpredict(seed): 0.622 Number of pairs reference - predicted secondary structure: 141 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Mastr(20) vs Vsfold5 Matthews Correlation Coefficient Mastr(20): 0.708 Vsfold5: 0.457 Sensitivity Mastr(20): 0.635 Vsfold5: 0.437 Positive Predictive Value Mastr(20): 0.793 Vsfold5: 0.484 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Mastr(20) vs RDfolder Matthews Correlation Coefficient Mastr(20): 0.730 RDfolder: 0.556 Sensitivity Mastr(20): 0.677 RDfolder: 0.511 Positive Predictive Value Mastr(20): 0.790 RDfolder: 0.611 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Mastr(20) vs MCFold Matthews Correlation Coefficient Mastr(20): 0.710 MCFold: 0.500 Sensitivity Mastr(20): 0.637 MCFold: 0.559 Positive Predictive Value Mastr(20): 0.796 MCFold: 0.453 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Mastr(20) vs NanoFolder Matthews Correlation Coefficient Mastr(20): 0.704 NanoFolder: 0.337 Sensitivity Mastr(20): 0.599 NanoFolder: 0.391 Positive Predictive Value Mastr(20): 0.832 NanoFolder: 0.298 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Mastr(20) vs Mastr(seed) Matthews Correlation Coefficient Mastr(20): 0.680 Mastr(seed): 0.265 Sensitivity Mastr(20): 0.549 Mastr(seed): 0.087 Positive Predictive Value Mastr(20): 0.845 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 154 Wilcoxon single-rank test P-value: 3.56938820447e-08
Fold	882 ContextFold vs Fold Matthews Correlation Coefficient ContextFold: 0.779 Fold: 0.628 Sensitivity ContextFold: 0.741 Fold: 0.620 Positive Predictive Value ContextFold: 0.823 Fold: 0.641 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 TurboFold(20) vs Fold Matthews Correlation Coefficient TurboFold(20): 0.889 Fold: 0.712 Sensitivity TurboFold(20): 0.861 Fold: 0.710 Positive Predictive Value TurboFold(20): 0.919 Fold: 0.717 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	216 CentroidAlifold(seed) vs Fold Matthews Correlation Coefficient CentroidAlifold(seed): 0.790 Fold: 0.701 Sensitivity CentroidAlifold(seed): 0.699 Fold: 0.699 Positive Predictive Value CentroidAlifold(seed): 0.896 Fold: 0.706 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 CentroidHomfold‑LAST vs Fold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.736 Fold: 0.628 Sensitivity CentroidHomfold‑LAST: 0.665 Fold: 0.620 Positive Predictive Value CentroidHomfold‑LAST: 0.818 Fold: 0.641 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	498 PETfold_pre2.0(seed) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.879 Fold: 0.686 Sensitivity PETfold_pre2.0(seed): 0.825 Fold: 0.687 Positive Predictive Value PETfold_pre2.0(seed): 0.938 Fold: 0.689 Number of pairs reference - predicted secondary structure: 498 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 TurboFold(seed) vs Fold Matthews Correlation Coefficient TurboFold(seed): 0.798 Fold: 0.746 Sensitivity TurboFold(seed): 0.766 Fold: 0.739 Positive Predictive Value TurboFold(seed): 0.835 Fold: 0.756 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	233 MXScarna(seed) vs Fold Matthews Correlation Coefficient MXScarna(seed): 0.750 Fold: 0.692 Sensitivity MXScarna(seed): 0.712 Fold: 0.690 Positive Predictive Value MXScarna(seed): 0.793 Fold: 0.697 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 CentroidAlifold(20) vs Fold Matthews Correlation Coefficient CentroidAlifold(20): 0.849 Fold: 0.712 Sensitivity CentroidAlifold(20): 0.754 Fold: 0.710 Positive Predictive Value CentroidAlifold(20): 0.957 Fold: 0.717 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 PETfold_pre2.0(20) vs Fold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 Fold: 0.712 Sensitivity PETfold_pre2.0(20): 0.737 Fold: 0.710 Positive Predictive Value PETfold_pre2.0(20): 0.975 Fold: 0.717 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 MXScarna(20) vs Fold Matthews Correlation Coefficient MXScarna(20): 0.838 Fold: 0.712 Sensitivity MXScarna(20): 0.791 Fold: 0.710 Positive Predictive Value MXScarna(20): 0.891 Fold: 0.717 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	314 PPfold(20) vs Fold Matthews Correlation Coefficient PPfold(20): 0.839 Fold: 0.709 Sensitivity PPfold(20): 0.721 Fold: 0.707 Positive Predictive Value PPfold(20): 0.977 Fold: 0.715 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RNAalifold(20) vs Fold Matthews Correlation Coefficient RNAalifold(20): 0.816 Fold: 0.712 Sensitivity RNAalifold(20): 0.690 Fold: 0.710 Positive Predictive Value RNAalifold(20): 0.966 Fold: 0.717 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RSpredict(20) vs Fold Matthews Correlation Coefficient RSpredict(20): 0.789 Fold: 0.712 Sensitivity RSpredict(20): 0.693 Fold: 0.710 Positive Predictive Value RSpredict(20): 0.901 Fold: 0.717 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 IPknot vs Fold Matthews Correlation Coefficient IPknot: 0.694 Fold: 0.628 Sensitivity IPknot: 0.661 Fold: 0.620 Positive Predictive Value IPknot: 0.733 Fold: 0.641 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	311 Multilign(20) vs Fold Matthews Correlation Coefficient Multilign(20): 0.784 Fold: 0.708 Sensitivity Multilign(20): 0.697 Fold: 0.706 Positive Predictive Value Multilign(20): 0.885 Fold: 0.714 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 CentroidFold vs Fold Matthews Correlation Coefficient CentroidFold: 0.645 Fold: 0.628 Sensitivity CentroidFold: 0.612 Fold: 0.620 Positive Predictive Value CentroidFold: 0.684 Fold: 0.641 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 Contrafold vs Fold Matthews Correlation Coefficient Contrafold: 0.643 Fold: 0.628 Sensitivity Contrafold: 0.634 Fold: 0.620 Positive Predictive Value Contrafold: 0.657 Fold: 0.641 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	315 RNASampler(20) vs Fold Matthews Correlation Coefficient RNASampler(20): 0.770 Fold: 0.713 Sensitivity RNASampler(20): 0.622 Fold: 0.711 Positive Predictive Value RNASampler(20): 0.957 Fold: 0.718 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	319 Murlet(20) vs Fold Matthews Correlation Coefficient Murlet(20): 0.750 Fold: 0.713 Sensitivity Murlet(20): 0.619 Fold: 0.711 Positive Predictive Value Murlet(20): 0.913 Fold: 0.718 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 Fold vs CMfinder(seed) Matthews Correlation Coefficient Fold: 0.574 CMfinder(seed): 0.571 Sensitivity Fold: 0.550 CMfinder(seed): 0.439 Positive Predictive Value Fold: 0.603 CMfinder(seed): 0.747 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 0.518809073978	882 MaxExpect vs Fold Matthews Correlation Coefficient MaxExpect: 0.633 Fold: 0.628 Sensitivity MaxExpect: 0.617 Fold: 0.620 Positive Predictive Value MaxExpect: 0.654 Fold: 0.641 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	316 CMfinder(20) vs Fold Matthews Correlation Coefficient CMfinder(20): 0.735 Fold: 0.711 Sensitivity CMfinder(20): 0.603 Fold: 0.710 Positive Predictive Value CMfinder(20): 0.899 Fold: 0.716 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	881 CRWrnafold vs Fold Matthews Correlation Coefficient CRWrnafold: 0.630 Fold: 0.628 Sensitivity CRWrnafold: 0.618 Fold: 0.620 Positive Predictive Value CRWrnafold: 0.648 Fold: 0.641 Number of pairs reference - predicted secondary structure: 881 Wilcoxon single-rank test P-value: 0.00094449411354	882 ProbKnot vs Fold Matthews Correlation Coefficient ProbKnot: 0.630 Fold: 0.628 Sensitivity ProbKnot: 0.622 Fold: 0.620 Positive Predictive Value ProbKnot: 0.644 Fold: 0.641 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 1.27481660653e-07	320 Fold vs Mastr(20) Matthews Correlation Coefficient Fold: 0.712 Mastr(20): 0.708 Sensitivity Fold: 0.710 Mastr(20): 0.635 Positive Predictive Value Fold: 0.717 Mastr(20): 0.793 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 0.00778217989366		+ Fold vs UNAFold Matthews Correlation Coefficient Fold: 0.628 UNAFold: 0.620 Sensitivity Fold: 0.620 UNAFold: 0.605 Positive Predictive Value Fold: 0.641 UNAFold: 0.639 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs PknotsRG Matthews Correlation Coefficient Fold: 0.628 PknotsRG: 0.617 Sensitivity Fold: 0.620 PknotsRG: 0.610 Positive Predictive Value Fold: 0.641 PknotsRG: 0.630 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Sfold Matthews Correlation Coefficient Fold: 0.628 Sfold: 0.618 Sensitivity Fold: 0.620 Sfold: 0.581 Positive Predictive Value Fold: 0.641 Sfold: 0.663 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RNAalifold(seed) Matthews Correlation Coefficient Fold: 0.705 RNAalifold(seed): 0.610 Sensitivity Fold: 0.702 RNAalifold(seed): 0.404 Positive Predictive Value Fold: 0.712 RNAalifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RNAsubopt Matthews Correlation Coefficient Fold: 0.628 RNAsubopt: 0.615 Sensitivity Fold: 0.620 RNAsubopt: 0.609 Positive Predictive Value Fold: 0.641 RNAsubopt: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs HotKnots Matthews Correlation Coefficient Fold: 0.630 HotKnots: 0.613 Sensitivity Fold: 0.622 HotKnots: 0.607 Positive Predictive Value Fold: 0.643 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 875 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RNAfold Matthews Correlation Coefficient Fold: 0.628 RNAfold: 0.612 Sensitivity Fold: 0.620 RNAfold: 0.604 Positive Predictive Value Fold: 0.641 RNAfold: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RNAshapes Matthews Correlation Coefficient Fold: 0.628 RNAshapes: 0.612 Sensitivity Fold: 0.620 RNAshapes: 0.602 Positive Predictive Value Fold: 0.641 RNAshapes: 0.628 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RNASampler(seed) Matthews Correlation Coefficient Fold: 0.587 RNASampler(seed): 0.557 Sensitivity Fold: 0.564 RNASampler(seed): 0.389 Positive Predictive Value Fold: 0.616 RNASampler(seed): 0.802 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Afold Matthews Correlation Coefficient Fold: 0.617 Afold: 0.558 Sensitivity Fold: 0.599 Afold: 0.541 Positive Predictive Value Fold: 0.642 Afold: 0.582 Number of pairs reference - predicted secondary structure: 530 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Pknots Matthews Correlation Coefficient Fold: 0.633 Pknots: 0.606 Sensitivity Fold: 0.622 Pknots: 0.595 Positive Predictive Value Fold: 0.650 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs McQFold Matthews Correlation Coefficient Fold: 0.628 McQFold: 0.583 Sensitivity Fold: 0.620 McQFold: 0.557 Positive Predictive Value Fold: 0.641 McQFold: 0.616 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Carnac(20) Matthews Correlation Coefficient Fold: 0.712 Carnac(20): 0.675 Sensitivity Fold: 0.710 Carnac(20): 0.500 Positive Predictive Value Fold: 0.717 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RNASLOpt Matthews Correlation Coefficient Fold: 0.628 RNASLOpt: 0.562 Sensitivity Fold: 0.620 RNASLOpt: 0.521 Positive Predictive Value Fold: 0.641 RNASLOpt: 0.613 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Cylofold Matthews Correlation Coefficient Fold: 0.654 Cylofold: 0.577 Sensitivity Fold: 0.644 Cylofold: 0.554 Positive Predictive Value Fold: 0.670 Cylofold: 0.608 Number of pairs reference - predicted secondary structure: 796 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Multilign(seed) vs Fold Matthews Correlation Coefficient Multilign(seed): 0.485 Fold: 0.430 Sensitivity Multilign(seed): 0.386 Fold: 0.405 Positive Predictive Value Multilign(seed): 0.619 Fold: 0.468 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.82627677697e-08	+ Fold vs RNAwolf Matthews Correlation Coefficient Fold: 0.628 RNAwolf: 0.518 Sensitivity Fold: 0.620 RNAwolf: 0.523 Positive Predictive Value Fold: 0.641 RNAwolf: 0.520 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs PPfold(seed) Matthews Correlation Coefficient Fold: 0.737 PPfold(seed): 0.380 Sensitivity Fold: 0.737 PPfold(seed): 0.170 Positive Predictive Value Fold: 0.741 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Murlet(seed) Matthews Correlation Coefficient Fold: 0.620 Murlet(seed): 0.468 Sensitivity Fold: 0.599 Murlet(seed): 0.266 Positive Predictive Value Fold: 0.645 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Alterna Matthews Correlation Coefficient Fold: 0.633 Alterna: 0.552 Sensitivity Fold: 0.623 Alterna: 0.547 Positive Predictive Value Fold: 0.650 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Carnac(seed) Matthews Correlation Coefficient Fold: 0.657 Carnac(seed): 0.415 Sensitivity Fold: 0.645 Carnac(seed): 0.196 Positive Predictive Value Fold: 0.673 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Vsfold4 Matthews Correlation Coefficient Fold: 0.628 Vsfold4: 0.487 Sensitivity Fold: 0.620 Vsfold4: 0.447 Positive Predictive Value Fold: 0.641 Vsfold4: 0.537 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RSpredict(seed) Matthews Correlation Coefficient Fold: 0.701 RSpredict(seed): 0.373 Sensitivity Fold: 0.699 RSpredict(seed): 0.251 Positive Predictive Value Fold: 0.706 RSpredict(seed): 0.562 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Vsfold5 Matthews Correlation Coefficient Fold: 0.628 Vsfold5: 0.477 Sensitivity Fold: 0.620 Vsfold5: 0.450 Positive Predictive Value Fold: 0.641 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs RDfolder Matthews Correlation Coefficient Fold: 0.633 RDfolder: 0.520 Sensitivity Fold: 0.623 RDfolder: 0.464 Positive Predictive Value Fold: 0.650 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs MCFold Matthews Correlation Coefficient Fold: 0.635 MCFold: 0.473 Sensitivity Fold: 0.625 MCFold: 0.524 Positive Predictive Value Fold: 0.651 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs NanoFolder Matthews Correlation Coefficient Fold: 0.667 NanoFolder: 0.335 Sensitivity Fold: 0.655 NanoFolder: 0.384 Positive Predictive Value Fold: 0.683 NanoFolder: 0.301 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Fold vs Mastr(seed) Matthews Correlation Coefficient Fold: 0.691 Mastr(seed): 0.263 Sensitivity Fold: 0.690 Mastr(seed): 0.089 Positive Predictive Value Fold: 0.697 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08
UNAFold	882 ContextFold vs UNAFold Matthews Correlation Coefficient ContextFold: 0.779 UNAFold: 0.620 Sensitivity ContextFold: 0.741 UNAFold: 0.605 Positive Predictive Value ContextFold: 0.823 UNAFold: 0.639 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 TurboFold(20) vs UNAFold Matthews Correlation Coefficient TurboFold(20): 0.889 UNAFold: 0.708 Sensitivity TurboFold(20): 0.861 UNAFold: 0.696 Positive Predictive Value TurboFold(20): 0.919 UNAFold: 0.723 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	216 CentroidAlifold(seed) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.790 UNAFold: 0.702 Sensitivity CentroidAlifold(seed): 0.699 UNAFold: 0.695 Positive Predictive Value CentroidAlifold(seed): 0.896 UNAFold: 0.713 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 CentroidHomfold‑LAST vs UNAFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.736 UNAFold: 0.620 Sensitivity CentroidHomfold‑LAST: 0.665 UNAFold: 0.605 Positive Predictive Value CentroidHomfold‑LAST: 0.818 UNAFold: 0.639 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	498 PETfold_pre2.0(seed) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.879 UNAFold: 0.670 Sensitivity PETfold_pre2.0(seed): 0.825 UNAFold: 0.665 Positive Predictive Value PETfold_pre2.0(seed): 0.938 UNAFold: 0.680 Number of pairs reference - predicted secondary structure: 498 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 TurboFold(seed) vs UNAFold Matthews Correlation Coefficient TurboFold(seed): 0.798 UNAFold: 0.733 Sensitivity TurboFold(seed): 0.766 UNAFold: 0.719 Positive Predictive Value TurboFold(seed): 0.835 UNAFold: 0.751 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	233 MXScarna(seed) vs UNAFold Matthews Correlation Coefficient MXScarna(seed): 0.750 UNAFold: 0.689 Sensitivity MXScarna(seed): 0.712 UNAFold: 0.683 Positive Predictive Value MXScarna(seed): 0.793 UNAFold: 0.699 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 CentroidAlifold(20) vs UNAFold Matthews Correlation Coefficient CentroidAlifold(20): 0.849 UNAFold: 0.708 Sensitivity CentroidAlifold(20): 0.754 UNAFold: 0.696 Positive Predictive Value CentroidAlifold(20): 0.957 UNAFold: 0.723 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 PETfold_pre2.0(20) vs UNAFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 UNAFold: 0.708 Sensitivity PETfold_pre2.0(20): 0.737 UNAFold: 0.696 Positive Predictive Value PETfold_pre2.0(20): 0.975 UNAFold: 0.723 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 MXScarna(20) vs UNAFold Matthews Correlation Coefficient MXScarna(20): 0.838 UNAFold: 0.708 Sensitivity MXScarna(20): 0.791 UNAFold: 0.696 Positive Predictive Value MXScarna(20): 0.891 UNAFold: 0.723 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	314 PPfold(20) vs UNAFold Matthews Correlation Coefficient PPfold(20): 0.839 UNAFold: 0.706 Sensitivity PPfold(20): 0.721 UNAFold: 0.694 Positive Predictive Value PPfold(20): 0.977 UNAFold: 0.722 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RNAalifold(20) vs UNAFold Matthews Correlation Coefficient RNAalifold(20): 0.816 UNAFold: 0.708 Sensitivity RNAalifold(20): 0.690 UNAFold: 0.696 Positive Predictive Value RNAalifold(20): 0.966 UNAFold: 0.723 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RSpredict(20) vs UNAFold Matthews Correlation Coefficient RSpredict(20): 0.789 UNAFold: 0.708 Sensitivity RSpredict(20): 0.693 UNAFold: 0.696 Positive Predictive Value RSpredict(20): 0.901 UNAFold: 0.723 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 IPknot vs UNAFold Matthews Correlation Coefficient IPknot: 0.694 UNAFold: 0.620 Sensitivity IPknot: 0.661 UNAFold: 0.605 Positive Predictive Value IPknot: 0.733 UNAFold: 0.639 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	311 Multilign(20) vs UNAFold Matthews Correlation Coefficient Multilign(20): 0.784 UNAFold: 0.706 Sensitivity Multilign(20): 0.697 UNAFold: 0.695 Positive Predictive Value Multilign(20): 0.885 UNAFold: 0.721 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 CentroidFold vs UNAFold Matthews Correlation Coefficient CentroidFold: 0.645 UNAFold: 0.620 Sensitivity CentroidFold: 0.612 UNAFold: 0.605 Positive Predictive Value CentroidFold: 0.684 UNAFold: 0.639 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 Contrafold vs UNAFold Matthews Correlation Coefficient Contrafold: 0.643 UNAFold: 0.620 Sensitivity Contrafold: 0.634 UNAFold: 0.605 Positive Predictive Value Contrafold: 0.657 UNAFold: 0.639 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	315 RNASampler(20) vs UNAFold Matthews Correlation Coefficient RNASampler(20): 0.770 UNAFold: 0.708 Sensitivity RNASampler(20): 0.622 UNAFold: 0.696 Positive Predictive Value RNASampler(20): 0.957 UNAFold: 0.723 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	319 Murlet(20) vs UNAFold Matthews Correlation Coefficient Murlet(20): 0.750 UNAFold: 0.708 Sensitivity Murlet(20): 0.619 UNAFold: 0.697 Positive Predictive Value Murlet(20): 0.913 UNAFold: 0.724 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 UNAFold vs CMfinder(seed) Matthews Correlation Coefficient UNAFold: 0.581 CMfinder(seed): 0.571 Sensitivity UNAFold: 0.556 CMfinder(seed): 0.439 Positive Predictive Value UNAFold: 0.613 CMfinder(seed): 0.747 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 2.90292419552e-06	882 MaxExpect vs UNAFold Matthews Correlation Coefficient MaxExpect: 0.633 UNAFold: 0.620 Sensitivity MaxExpect: 0.617 UNAFold: 0.605 Positive Predictive Value MaxExpect: 0.654 UNAFold: 0.639 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	316 CMfinder(20) vs UNAFold Matthews Correlation Coefficient CMfinder(20): 0.735 UNAFold: 0.707 Sensitivity CMfinder(20): 0.603 UNAFold: 0.696 Positive Predictive Value CMfinder(20): 0.899 UNAFold: 0.722 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	881 CRWrnafold vs UNAFold Matthews Correlation Coefficient CRWrnafold: 0.630 UNAFold: 0.619 Sensitivity CRWrnafold: 0.618 UNAFold: 0.605 Positive Predictive Value CRWrnafold: 0.648 UNAFold: 0.639 Number of pairs reference - predicted secondary structure: 881 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 ProbKnot vs UNAFold Matthews Correlation Coefficient ProbKnot: 0.630 UNAFold: 0.620 Sensitivity ProbKnot: 0.622 UNAFold: 0.605 Positive Predictive Value ProbKnot: 0.644 UNAFold: 0.639 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 Mastr(20) vs UNAFold Matthews Correlation Coefficient Mastr(20): 0.708 UNAFold: 0.708 Sensitivity Mastr(20): 0.635 UNAFold: 0.696 Positive Predictive Value Mastr(20): 0.793 UNAFold: 0.723 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 0.600132072507	882 Fold vs UNAFold Matthews Correlation Coefficient Fold: 0.628 UNAFold: 0.620 Sensitivity Fold: 0.620 UNAFold: 0.605 Positive Predictive Value Fold: 0.641 UNAFold: 0.639 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ UNAFold vs PknotsRG Matthews Correlation Coefficient UNAFold: 0.620 PknotsRG: 0.617 Sensitivity UNAFold: 0.605 PknotsRG: 0.610 Positive Predictive Value UNAFold: 0.639 PknotsRG: 0.630 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 1.03971108356e-05	+ UNAFold vs Sfold Matthews Correlation Coefficient UNAFold: 0.620 Sfold: 0.618 Sensitivity UNAFold: 0.605 Sfold: 0.581 Positive Predictive Value UNAFold: 0.639 Sfold: 0.663 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 0.000672262794322	+ UNAFold vs RNAalifold(seed) Matthews Correlation Coefficient UNAFold: 0.711 RNAalifold(seed): 0.610 Sensitivity UNAFold: 0.701 RNAalifold(seed): 0.404 Positive Predictive Value UNAFold: 0.724 RNAalifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RNAsubopt Matthews Correlation Coefficient UNAFold: 0.620 RNAsubopt: 0.615 Sensitivity UNAFold: 0.605 RNAsubopt: 0.609 Positive Predictive Value UNAFold: 0.639 RNAsubopt: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 5.62644058675e-08	+ UNAFold vs HotKnots Matthews Correlation Coefficient UNAFold: 0.618 HotKnots: 0.613 Sensitivity UNAFold: 0.603 HotKnots: 0.607 Positive Predictive Value UNAFold: 0.638 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 875 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RNAfold Matthews Correlation Coefficient UNAFold: 0.620 RNAfold: 0.612 Sensitivity UNAFold: 0.605 RNAfold: 0.604 Positive Predictive Value UNAFold: 0.639 RNAfold: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RNAshapes Matthews Correlation Coefficient UNAFold: 0.620 RNAshapes: 0.612 Sensitivity UNAFold: 0.605 RNAshapes: 0.602 Positive Predictive Value UNAFold: 0.639 RNAshapes: 0.628 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RNASampler(seed) Matthews Correlation Coefficient UNAFold: 0.597 RNASampler(seed): 0.557 Sensitivity UNAFold: 0.570 RNASampler(seed): 0.389 Positive Predictive Value UNAFold: 0.629 RNASampler(seed): 0.802 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Afold Matthews Correlation Coefficient UNAFold: 0.624 Afold: 0.558 Sensitivity UNAFold: 0.597 Afold: 0.541 Positive Predictive Value UNAFold: 0.658 Afold: 0.582 Number of pairs reference - predicted secondary structure: 530 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Pknots vs UNAFold Matthews Correlation Coefficient Pknots: 0.606 UNAFold: 0.596 Sensitivity Pknots: 0.595 UNAFold: 0.583 Positive Predictive Value Pknots: 0.624 UNAFold: 0.616 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs McQFold Matthews Correlation Coefficient UNAFold: 0.620 McQFold: 0.583 Sensitivity UNAFold: 0.605 McQFold: 0.557 Positive Predictive Value UNAFold: 0.639 McQFold: 0.616 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Carnac(20) Matthews Correlation Coefficient UNAFold: 0.708 Carnac(20): 0.675 Sensitivity UNAFold: 0.696 Carnac(20): 0.500 Positive Predictive Value UNAFold: 0.723 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RNASLOpt Matthews Correlation Coefficient UNAFold: 0.620 RNASLOpt: 0.562 Sensitivity UNAFold: 0.605 RNASLOpt: 0.521 Positive Predictive Value UNAFold: 0.639 RNASLOpt: 0.613 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Cylofold Matthews Correlation Coefficient UNAFold: 0.641 Cylofold: 0.577 Sensitivity UNAFold: 0.625 Cylofold: 0.554 Positive Predictive Value UNAFold: 0.662 Cylofold: 0.608 Number of pairs reference - predicted secondary structure: 796 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Multilign(seed) vs UNAFold Matthews Correlation Coefficient Multilign(seed): 0.485 UNAFold: 0.469 Sensitivity Multilign(seed): 0.386 UNAFold: 0.437 Positive Predictive Value Multilign(seed): 0.619 UNAFold: 0.514 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 5.59774301112e-05	+ UNAFold vs RNAwolf Matthews Correlation Coefficient UNAFold: 0.620 RNAwolf: 0.518 Sensitivity UNAFold: 0.605 RNAwolf: 0.523 Positive Predictive Value UNAFold: 0.639 RNAwolf: 0.520 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs PPfold(seed) Matthews Correlation Coefficient UNAFold: 0.688 PPfold(seed): 0.380 Sensitivity UNAFold: 0.685 PPfold(seed): 0.170 Positive Predictive Value UNAFold: 0.696 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Murlet(seed) Matthews Correlation Coefficient UNAFold: 0.628 Murlet(seed): 0.468 Sensitivity UNAFold: 0.604 Murlet(seed): 0.266 Positive Predictive Value UNAFold: 0.657 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Alterna Matthews Correlation Coefficient UNAFold: 0.597 Alterna: 0.552 Sensitivity UNAFold: 0.584 Alterna: 0.547 Positive Predictive Value UNAFold: 0.617 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Carnac(seed) Matthews Correlation Coefficient UNAFold: 0.655 Carnac(seed): 0.415 Sensitivity UNAFold: 0.640 Carnac(seed): 0.196 Positive Predictive Value UNAFold: 0.674 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Vsfold4 Matthews Correlation Coefficient UNAFold: 0.620 Vsfold4: 0.487 Sensitivity UNAFold: 0.605 Vsfold4: 0.447 Positive Predictive Value UNAFold: 0.639 Vsfold4: 0.537 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RSpredict(seed) Matthews Correlation Coefficient UNAFold: 0.702 RSpredict(seed): 0.373 Sensitivity UNAFold: 0.695 RSpredict(seed): 0.251 Positive Predictive Value UNAFold: 0.713 RSpredict(seed): 0.562 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Vsfold5 Matthews Correlation Coefficient UNAFold: 0.620 Vsfold5: 0.477 Sensitivity UNAFold: 0.605 Vsfold5: 0.450 Positive Predictive Value UNAFold: 0.639 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs RDfolder Matthews Correlation Coefficient UNAFold: 0.597 RDfolder: 0.520 Sensitivity UNAFold: 0.584 RDfolder: 0.464 Positive Predictive Value UNAFold: 0.617 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs MCFold Matthews Correlation Coefficient UNAFold: 0.618 MCFold: 0.473 Sensitivity UNAFold: 0.601 MCFold: 0.524 Positive Predictive Value UNAFold: 0.640 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs NanoFolder Matthews Correlation Coefficient UNAFold: 0.670 NanoFolder: 0.335 Sensitivity UNAFold: 0.654 NanoFolder: 0.384 Positive Predictive Value UNAFold: 0.691 NanoFolder: 0.301 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ UNAFold vs Mastr(seed) Matthews Correlation Coefficient UNAFold: 0.690 Mastr(seed): 0.263 Sensitivity UNAFold: 0.684 Mastr(seed): 0.089 Positive Predictive Value UNAFold: 0.700 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08
PknotsRG	882 ContextFold vs PknotsRG Matthews Correlation Coefficient ContextFold: 0.779 PknotsRG: 0.617 Sensitivity ContextFold: 0.741 PknotsRG: 0.610 Positive Predictive Value ContextFold: 0.823 PknotsRG: 0.630 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 TurboFold(20) vs PknotsRG Matthews Correlation Coefficient TurboFold(20): 0.889 PknotsRG: 0.691 Sensitivity TurboFold(20): 0.861 PknotsRG: 0.687 Positive Predictive Value TurboFold(20): 0.919 PknotsRG: 0.699 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	216 CentroidAlifold(seed) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(seed): 0.790 PknotsRG: 0.705 Sensitivity CentroidAlifold(seed): 0.699 PknotsRG: 0.705 Positive Predictive Value CentroidAlifold(seed): 0.896 PknotsRG: 0.710 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 CentroidHomfold‑LAST vs PknotsRG Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.736 PknotsRG: 0.617 Sensitivity CentroidHomfold‑LAST: 0.665 PknotsRG: 0.610 Positive Predictive Value CentroidHomfold‑LAST: 0.818 PknotsRG: 0.630 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	498 PETfold_pre2.0(seed) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.879 PknotsRG: 0.670 Sensitivity PETfold_pre2.0(seed): 0.825 PknotsRG: 0.671 Positive Predictive Value PETfold_pre2.0(seed): 0.938 PknotsRG: 0.673 Number of pairs reference - predicted secondary structure: 498 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 PknotsRG vs TurboFold(seed) Matthews Correlation Coefficient PknotsRG: 0.830 TurboFold(seed): 0.798 Sensitivity PknotsRG: 0.826 TurboFold(seed): 0.766 Positive Predictive Value PknotsRG: 0.837 TurboFold(seed): 0.835 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	233 MXScarna(seed) vs PknotsRG Matthews Correlation Coefficient MXScarna(seed): 0.750 PknotsRG: 0.693 Sensitivity MXScarna(seed): 0.712 PknotsRG: 0.692 Positive Predictive Value MXScarna(seed): 0.793 PknotsRG: 0.697 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 CentroidAlifold(20) vs PknotsRG Matthews Correlation Coefficient CentroidAlifold(20): 0.849 PknotsRG: 0.691 Sensitivity CentroidAlifold(20): 0.754 PknotsRG: 0.687 Positive Predictive Value CentroidAlifold(20): 0.957 PknotsRG: 0.699 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 PETfold_pre2.0(20) vs PknotsRG Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 PknotsRG: 0.691 Sensitivity PETfold_pre2.0(20): 0.737 PknotsRG: 0.687 Positive Predictive Value PETfold_pre2.0(20): 0.975 PknotsRG: 0.699 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 MXScarna(20) vs PknotsRG Matthews Correlation Coefficient MXScarna(20): 0.838 PknotsRG: 0.691 Sensitivity MXScarna(20): 0.791 PknotsRG: 0.687 Positive Predictive Value MXScarna(20): 0.891 PknotsRG: 0.699 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	314 PPfold(20) vs PknotsRG Matthews Correlation Coefficient PPfold(20): 0.839 PknotsRG: 0.689 Sensitivity PPfold(20): 0.721 PknotsRG: 0.685 Positive Predictive Value PPfold(20): 0.977 PknotsRG: 0.697 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RNAalifold(20) vs PknotsRG Matthews Correlation Coefficient RNAalifold(20): 0.816 PknotsRG: 0.691 Sensitivity RNAalifold(20): 0.690 PknotsRG: 0.687 Positive Predictive Value RNAalifold(20): 0.966 PknotsRG: 0.699 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RSpredict(20) vs PknotsRG Matthews Correlation Coefficient RSpredict(20): 0.789 PknotsRG: 0.691 Sensitivity RSpredict(20): 0.693 PknotsRG: 0.687 Positive Predictive Value RSpredict(20): 0.901 PknotsRG: 0.699 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 IPknot vs PknotsRG Matthews Correlation Coefficient IPknot: 0.694 PknotsRG: 0.617 Sensitivity IPknot: 0.661 PknotsRG: 0.610 Positive Predictive Value IPknot: 0.733 PknotsRG: 0.630 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	311 Multilign(20) vs PknotsRG Matthews Correlation Coefficient Multilign(20): 0.784 PknotsRG: 0.688 Sensitivity Multilign(20): 0.697 PknotsRG: 0.684 Positive Predictive Value Multilign(20): 0.885 PknotsRG: 0.696 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 CentroidFold vs PknotsRG Matthews Correlation Coefficient CentroidFold: 0.645 PknotsRG: 0.617 Sensitivity CentroidFold: 0.612 PknotsRG: 0.610 Positive Predictive Value CentroidFold: 0.684 PknotsRG: 0.630 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 Contrafold vs PknotsRG Matthews Correlation Coefficient Contrafold: 0.643 PknotsRG: 0.617 Sensitivity Contrafold: 0.634 PknotsRG: 0.610 Positive Predictive Value Contrafold: 0.657 PknotsRG: 0.630 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	315 RNASampler(20) vs PknotsRG Matthews Correlation Coefficient RNASampler(20): 0.770 PknotsRG: 0.691 Sensitivity RNASampler(20): 0.622 PknotsRG: 0.687 Positive Predictive Value RNASampler(20): 0.957 PknotsRG: 0.699 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	319 Murlet(20) vs PknotsRG Matthews Correlation Coefficient Murlet(20): 0.750 PknotsRG: 0.692 Sensitivity Murlet(20): 0.619 PknotsRG: 0.688 Positive Predictive Value Murlet(20): 0.913 PknotsRG: 0.700 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 PknotsRG vs CMfinder(seed) Matthews Correlation Coefficient PknotsRG: 0.598 CMfinder(seed): 0.571 Sensitivity PknotsRG: 0.582 CMfinder(seed): 0.439 Positive Predictive Value PknotsRG: 0.619 CMfinder(seed): 0.747 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 5.21776328505e-08	882 MaxExpect vs PknotsRG Matthews Correlation Coefficient MaxExpect: 0.633 PknotsRG: 0.617 Sensitivity MaxExpect: 0.617 PknotsRG: 0.610 Positive Predictive Value MaxExpect: 0.654 PknotsRG: 0.630 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	316 CMfinder(20) vs PknotsRG Matthews Correlation Coefficient CMfinder(20): 0.735 PknotsRG: 0.689 Sensitivity CMfinder(20): 0.603 PknotsRG: 0.685 Positive Predictive Value CMfinder(20): 0.899 PknotsRG: 0.696 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	881 CRWrnafold vs PknotsRG Matthews Correlation Coefficient CRWrnafold: 0.630 PknotsRG: 0.617 Sensitivity CRWrnafold: 0.618 PknotsRG: 0.610 Positive Predictive Value CRWrnafold: 0.648 PknotsRG: 0.630 Number of pairs reference - predicted secondary structure: 881 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 ProbKnot vs PknotsRG Matthews Correlation Coefficient ProbKnot: 0.630 PknotsRG: 0.617 Sensitivity ProbKnot: 0.622 PknotsRG: 0.610 Positive Predictive Value ProbKnot: 0.644 PknotsRG: 0.630 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 Mastr(20) vs PknotsRG Matthews Correlation Coefficient Mastr(20): 0.708 PknotsRG: 0.691 Sensitivity Mastr(20): 0.635 PknotsRG: 0.687 Positive Predictive Value Mastr(20): 0.793 PknotsRG: 0.699 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 Fold vs PknotsRG Matthews Correlation Coefficient Fold: 0.628 PknotsRG: 0.617 Sensitivity Fold: 0.620 PknotsRG: 0.610 Positive Predictive Value Fold: 0.641 PknotsRG: 0.630 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 UNAFold vs PknotsRG Matthews Correlation Coefficient UNAFold: 0.620 PknotsRG: 0.617 Sensitivity UNAFold: 0.605 PknotsRG: 0.610 Positive Predictive Value UNAFold: 0.639 PknotsRG: 0.630 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 1.03971108356e-05		- Sfold vs PknotsRG Matthews Correlation Coefficient Sfold: 0.618 PknotsRG: 0.617 Sensitivity Sfold: 0.581 PknotsRG: 0.610 Positive Predictive Value Sfold: 0.663 PknotsRG: 0.630 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.90487810335e-05	+ PknotsRG vs RNAalifold(seed) Matthews Correlation Coefficient PknotsRG: 0.714 RNAalifold(seed): 0.610 Sensitivity PknotsRG: 0.711 RNAalifold(seed): 0.404 Positive Predictive Value PknotsRG: 0.720 RNAalifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RNAsubopt Matthews Correlation Coefficient PknotsRG: 0.617 RNAsubopt: 0.615 Sensitivity PknotsRG: 0.610 RNAsubopt: 0.609 Positive Predictive Value PknotsRG: 0.630 RNAsubopt: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.76761760679e-06	+ PknotsRG vs HotKnots Matthews Correlation Coefficient PknotsRG: 0.617 HotKnots: 0.613 Sensitivity PknotsRG: 0.610 HotKnots: 0.607 Positive Predictive Value PknotsRG: 0.630 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 875 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ PknotsRG vs RNAfold Matthews Correlation Coefficient PknotsRG: 0.617 RNAfold: 0.612 Sensitivity PknotsRG: 0.610 RNAfold: 0.604 Positive Predictive Value PknotsRG: 0.630 RNAfold: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RNAshapes Matthews Correlation Coefficient PknotsRG: 0.617 RNAshapes: 0.612 Sensitivity PknotsRG: 0.610 RNAshapes: 0.602 Positive Predictive Value PknotsRG: 0.630 RNAshapes: 0.628 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RNASampler(seed) Matthews Correlation Coefficient PknotsRG: 0.622 RNASampler(seed): 0.557 Sensitivity PknotsRG: 0.606 RNASampler(seed): 0.389 Positive Predictive Value PknotsRG: 0.643 RNASampler(seed): 0.802 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Afold Matthews Correlation Coefficient PknotsRG: 0.622 Afold: 0.558 Sensitivity PknotsRG: 0.602 Afold: 0.541 Positive Predictive Value PknotsRG: 0.649 Afold: 0.582 Number of pairs reference - predicted secondary structure: 530 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Pknots vs PknotsRG Matthews Correlation Coefficient Pknots: 0.606 PknotsRG: 0.603 Sensitivity Pknots: 0.595 PknotsRG: 0.595 Positive Predictive Value Pknots: 0.624 PknotsRG: 0.617 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 8.10048797242e-06	+ PknotsRG vs McQFold Matthews Correlation Coefficient PknotsRG: 0.617 McQFold: 0.583 Sensitivity PknotsRG: 0.610 McQFold: 0.557 Positive Predictive Value PknotsRG: 0.630 McQFold: 0.616 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Carnac(20) Matthews Correlation Coefficient PknotsRG: 0.691 Carnac(20): 0.675 Sensitivity PknotsRG: 0.687 Carnac(20): 0.500 Positive Predictive Value PknotsRG: 0.699 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ PknotsRG vs RNASLOpt Matthews Correlation Coefficient PknotsRG: 0.617 RNASLOpt: 0.562 Sensitivity PknotsRG: 0.610 RNASLOpt: 0.521 Positive Predictive Value PknotsRG: 0.630 RNASLOpt: 0.613 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Cylofold Matthews Correlation Coefficient PknotsRG: 0.639 Cylofold: 0.577 Sensitivity PknotsRG: 0.630 Cylofold: 0.554 Positive Predictive Value PknotsRG: 0.654 Cylofold: 0.608 Number of pairs reference - predicted secondary structure: 796 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Multilign(seed) Matthews Correlation Coefficient PknotsRG: 0.742 Multilign(seed): 0.485 Sensitivity PknotsRG: 0.716 Multilign(seed): 0.386 Positive Predictive Value PknotsRG: 0.774 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.57237423209e-08	+ PknotsRG vs RNAwolf Matthews Correlation Coefficient PknotsRG: 0.617 RNAwolf: 0.518 Sensitivity PknotsRG: 0.610 RNAwolf: 0.523 Positive Predictive Value PknotsRG: 0.630 RNAwolf: 0.520 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs PPfold(seed) Matthews Correlation Coefficient PknotsRG: 0.752 PPfold(seed): 0.380 Sensitivity PknotsRG: 0.756 PPfold(seed): 0.170 Positive Predictive Value PknotsRG: 0.751 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Murlet(seed) Matthews Correlation Coefficient PknotsRG: 0.649 Murlet(seed): 0.468 Sensitivity PknotsRG: 0.635 Murlet(seed): 0.266 Positive Predictive Value PknotsRG: 0.668 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Alterna Matthews Correlation Coefficient PknotsRG: 0.605 Alterna: 0.552 Sensitivity PknotsRG: 0.598 Alterna: 0.547 Positive Predictive Value PknotsRG: 0.619 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Carnac(seed) Matthews Correlation Coefficient PknotsRG: 0.668 Carnac(seed): 0.415 Sensitivity PknotsRG: 0.661 Carnac(seed): 0.196 Positive Predictive Value PknotsRG: 0.679 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Vsfold4 Matthews Correlation Coefficient PknotsRG: 0.617 Vsfold4: 0.487 Sensitivity PknotsRG: 0.610 Vsfold4: 0.447 Positive Predictive Value PknotsRG: 0.630 Vsfold4: 0.537 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RSpredict(seed) Matthews Correlation Coefficient PknotsRG: 0.705 RSpredict(seed): 0.373 Sensitivity PknotsRG: 0.705 RSpredict(seed): 0.251 Positive Predictive Value PknotsRG: 0.710 RSpredict(seed): 0.562 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Vsfold5 Matthews Correlation Coefficient PknotsRG: 0.617 Vsfold5: 0.477 Sensitivity PknotsRG: 0.610 Vsfold5: 0.450 Positive Predictive Value PknotsRG: 0.630 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs RDfolder Matthews Correlation Coefficient PknotsRG: 0.605 RDfolder: 0.520 Sensitivity PknotsRG: 0.598 RDfolder: 0.464 Positive Predictive Value PknotsRG: 0.619 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs MCFold Matthews Correlation Coefficient PknotsRG: 0.620 MCFold: 0.473 Sensitivity PknotsRG: 0.610 MCFold: 0.524 Positive Predictive Value PknotsRG: 0.635 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs NanoFolder Matthews Correlation Coefficient PknotsRG: 0.662 NanoFolder: 0.335 Sensitivity PknotsRG: 0.650 NanoFolder: 0.384 Positive Predictive Value PknotsRG: 0.679 NanoFolder: 0.301 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PknotsRG vs Mastr(seed) Matthews Correlation Coefficient PknotsRG: 0.693 Mastr(seed): 0.263 Sensitivity PknotsRG: 0.692 Mastr(seed): 0.089 Positive Predictive Value PknotsRG: 0.697 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08
Sfold	882 ContextFold vs Sfold Matthews Correlation Coefficient ContextFold: 0.779 Sfold: 0.618 Sensitivity ContextFold: 0.741 Sfold: 0.581 Positive Predictive Value ContextFold: 0.823 Sfold: 0.663 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 TurboFold(20) vs Sfold Matthews Correlation Coefficient TurboFold(20): 0.889 Sfold: 0.698 Sensitivity TurboFold(20): 0.861 Sfold: 0.662 Positive Predictive Value TurboFold(20): 0.919 Sfold: 0.740 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	216 CentroidAlifold(seed) vs Sfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.790 Sfold: 0.686 Sensitivity CentroidAlifold(seed): 0.699 Sfold: 0.656 Positive Predictive Value CentroidAlifold(seed): 0.896 Sfold: 0.721 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 CentroidHomfold‑LAST vs Sfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.736 Sfold: 0.618 Sensitivity CentroidHomfold‑LAST: 0.665 Sfold: 0.581 Positive Predictive Value CentroidHomfold‑LAST: 0.818 Sfold: 0.663 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	498 PETfold_pre2.0(seed) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.879 Sfold: 0.667 Sensitivity PETfold_pre2.0(seed): 0.825 Sfold: 0.635 Positive Predictive Value PETfold_pre2.0(seed): 0.938 Sfold: 0.705 Number of pairs reference - predicted secondary structure: 498 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 TurboFold(seed) vs Sfold Matthews Correlation Coefficient TurboFold(seed): 0.798 Sfold: 0.725 Sensitivity TurboFold(seed): 0.766 Sfold: 0.705 Positive Predictive Value TurboFold(seed): 0.835 Sfold: 0.750 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	233 MXScarna(seed) vs Sfold Matthews Correlation Coefficient MXScarna(seed): 0.750 Sfold: 0.680 Sensitivity MXScarna(seed): 0.712 Sfold: 0.648 Positive Predictive Value MXScarna(seed): 0.793 Sfold: 0.718 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 CentroidAlifold(20) vs Sfold Matthews Correlation Coefficient CentroidAlifold(20): 0.849 Sfold: 0.698 Sensitivity CentroidAlifold(20): 0.754 Sfold: 0.662 Positive Predictive Value CentroidAlifold(20): 0.957 Sfold: 0.740 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 PETfold_pre2.0(20) vs Sfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 Sfold: 0.698 Sensitivity PETfold_pre2.0(20): 0.737 Sfold: 0.662 Positive Predictive Value PETfold_pre2.0(20): 0.975 Sfold: 0.740 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 MXScarna(20) vs Sfold Matthews Correlation Coefficient MXScarna(20): 0.838 Sfold: 0.698 Sensitivity MXScarna(20): 0.791 Sfold: 0.662 Positive Predictive Value MXScarna(20): 0.891 Sfold: 0.740 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	314 PPfold(20) vs Sfold Matthews Correlation Coefficient PPfold(20): 0.839 Sfold: 0.698 Sensitivity PPfold(20): 0.721 Sfold: 0.661 Positive Predictive Value PPfold(20): 0.977 Sfold: 0.741 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RNAalifold(20) vs Sfold Matthews Correlation Coefficient RNAalifold(20): 0.816 Sfold: 0.698 Sensitivity RNAalifold(20): 0.690 Sfold: 0.662 Positive Predictive Value RNAalifold(20): 0.966 Sfold: 0.740 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RSpredict(20) vs Sfold Matthews Correlation Coefficient RSpredict(20): 0.789 Sfold: 0.698 Sensitivity RSpredict(20): 0.693 Sfold: 0.662 Positive Predictive Value RSpredict(20): 0.901 Sfold: 0.740 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 IPknot vs Sfold Matthews Correlation Coefficient IPknot: 0.694 Sfold: 0.618 Sensitivity IPknot: 0.661 Sfold: 0.581 Positive Predictive Value IPknot: 0.733 Sfold: 0.663 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	311 Multilign(20) vs Sfold Matthews Correlation Coefficient Multilign(20): 0.784 Sfold: 0.696 Sensitivity Multilign(20): 0.697 Sfold: 0.660 Positive Predictive Value Multilign(20): 0.885 Sfold: 0.738 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 CentroidFold vs Sfold Matthews Correlation Coefficient CentroidFold: 0.645 Sfold: 0.618 Sensitivity CentroidFold: 0.612 Sfold: 0.581 Positive Predictive Value CentroidFold: 0.684 Sfold: 0.663 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 Contrafold vs Sfold Matthews Correlation Coefficient Contrafold: 0.643 Sfold: 0.618 Sensitivity Contrafold: 0.634 Sfold: 0.581 Positive Predictive Value Contrafold: 0.657 Sfold: 0.663 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	315 RNASampler(20) vs Sfold Matthews Correlation Coefficient RNASampler(20): 0.770 Sfold: 0.700 Sensitivity RNASampler(20): 0.622 Sfold: 0.664 Positive Predictive Value RNASampler(20): 0.957 Sfold: 0.743 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	319 Murlet(20) vs Sfold Matthews Correlation Coefficient Murlet(20): 0.750 Sfold: 0.699 Sensitivity Murlet(20): 0.619 Sfold: 0.663 Positive Predictive Value Murlet(20): 0.913 Sfold: 0.741 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 CMfinder(seed) vs Sfold Matthews Correlation Coefficient CMfinder(seed): 0.571 Sfold: 0.545 Sensitivity CMfinder(seed): 0.439 Sfold: 0.497 Positive Predictive Value CMfinder(seed): 0.747 Sfold: 0.604 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 5.62644058675e-08	882 MaxExpect vs Sfold Matthews Correlation Coefficient MaxExpect: 0.633 Sfold: 0.618 Sensitivity MaxExpect: 0.617 Sfold: 0.581 Positive Predictive Value MaxExpect: 0.654 Sfold: 0.663 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	316 CMfinder(20) vs Sfold Matthews Correlation Coefficient CMfinder(20): 0.735 Sfold: 0.698 Sensitivity CMfinder(20): 0.603 Sfold: 0.662 Positive Predictive Value CMfinder(20): 0.899 Sfold: 0.739 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	881 CRWrnafold vs Sfold Matthews Correlation Coefficient CRWrnafold: 0.630 Sfold: 0.618 Sensitivity CRWrnafold: 0.618 Sfold: 0.581 Positive Predictive Value CRWrnafold: 0.648 Sfold: 0.663 Number of pairs reference - predicted secondary structure: 881 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 ProbKnot vs Sfold Matthews Correlation Coefficient ProbKnot: 0.630 Sfold: 0.618 Sensitivity ProbKnot: 0.622 Sfold: 0.581 Positive Predictive Value ProbKnot: 0.644 Sfold: 0.663 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 Mastr(20) vs Sfold Matthews Correlation Coefficient Mastr(20): 0.708 Sfold: 0.698 Sensitivity Mastr(20): 0.635 Sfold: 0.662 Positive Predictive Value Mastr(20): 0.793 Sfold: 0.740 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 5.21776328505e-08	882 Fold vs Sfold Matthews Correlation Coefficient Fold: 0.628 Sfold: 0.618 Sensitivity Fold: 0.620 Sfold: 0.581 Positive Predictive Value Fold: 0.641 Sfold: 0.663 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 UNAFold vs Sfold Matthews Correlation Coefficient UNAFold: 0.620 Sfold: 0.618 Sensitivity UNAFold: 0.605 Sfold: 0.581 Positive Predictive Value UNAFold: 0.639 Sfold: 0.663 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 0.000672262794322	882 Sfold vs PknotsRG Matthews Correlation Coefficient Sfold: 0.618 PknotsRG: 0.617 Sensitivity Sfold: 0.581 PknotsRG: 0.610 Positive Predictive Value Sfold: 0.663 PknotsRG: 0.630 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.90487810335e-05		+ Sfold vs RNAalifold(seed) Matthews Correlation Coefficient Sfold: 0.690 RNAalifold(seed): 0.610 Sensitivity Sfold: 0.658 RNAalifold(seed): 0.404 Positive Predictive Value Sfold: 0.727 RNAalifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNAsubopt Matthews Correlation Coefficient Sfold: 0.618 RNAsubopt: 0.615 Sensitivity Sfold: 0.581 RNAsubopt: 0.609 Positive Predictive Value Sfold: 0.663 RNAsubopt: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ Sfold vs HotKnots Matthews Correlation Coefficient Sfold: 0.617 HotKnots: 0.613 Sensitivity Sfold: 0.581 HotKnots: 0.607 Positive Predictive Value Sfold: 0.662 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 875 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNAfold Matthews Correlation Coefficient Sfold: 0.618 RNAfold: 0.612 Sensitivity Sfold: 0.581 RNAfold: 0.604 Positive Predictive Value Sfold: 0.663 RNAfold: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNAshapes Matthews Correlation Coefficient Sfold: 0.618 RNAshapes: 0.612 Sensitivity Sfold: 0.581 RNAshapes: 0.602 Positive Predictive Value Sfold: 0.663 RNAshapes: 0.628 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNASampler(seed) Matthews Correlation Coefficient Sfold: 0.565 RNASampler(seed): 0.557 Sensitivity Sfold: 0.516 RNASampler(seed): 0.389 Positive Predictive Value Sfold: 0.625 RNASampler(seed): 0.802 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 9.69999390915e-05	+ Sfold vs Afold Matthews Correlation Coefficient Sfold: 0.619 Afold: 0.558 Sensitivity Sfold: 0.574 Afold: 0.541 Positive Predictive Value Sfold: 0.673 Afold: 0.582 Number of pairs reference - predicted secondary structure: 530 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Pknots vs Sfold Matthews Correlation Coefficient Pknots: 0.606 Sfold: 0.601 Sensitivity Pknots: 0.595 Sfold: 0.565 Positive Predictive Value Pknots: 0.624 Sfold: 0.648 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 1.70738736246e-07	+ Sfold vs McQFold Matthews Correlation Coefficient Sfold: 0.618 McQFold: 0.583 Sensitivity Sfold: 0.581 McQFold: 0.557 Positive Predictive Value Sfold: 0.663 McQFold: 0.616 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Carnac(20) Matthews Correlation Coefficient Sfold: 0.698 Carnac(20): 0.675 Sensitivity Sfold: 0.662 Carnac(20): 0.500 Positive Predictive Value Sfold: 0.740 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RNASLOpt Matthews Correlation Coefficient Sfold: 0.618 RNASLOpt: 0.562 Sensitivity Sfold: 0.581 RNASLOpt: 0.521 Positive Predictive Value Sfold: 0.663 RNASLOpt: 0.613 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Cylofold Matthews Correlation Coefficient Sfold: 0.641 Cylofold: 0.577 Sensitivity Sfold: 0.604 Cylofold: 0.554 Positive Predictive Value Sfold: 0.687 Cylofold: 0.608 Number of pairs reference - predicted secondary structure: 796 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Multilign(seed) vs Sfold Matthews Correlation Coefficient Multilign(seed): 0.485 Sfold: 0.456 Sensitivity Multilign(seed): 0.386 Sfold: 0.414 Positive Predictive Value Multilign(seed): 0.619 Sfold: 0.511 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 8.95709882289e-08	+ Sfold vs RNAwolf Matthews Correlation Coefficient Sfold: 0.618 RNAwolf: 0.518 Sensitivity Sfold: 0.581 RNAwolf: 0.523 Positive Predictive Value Sfold: 0.663 RNAwolf: 0.520 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs PPfold(seed) Matthews Correlation Coefficient Sfold: 0.709 PPfold(seed): 0.380 Sensitivity Sfold: 0.686 PPfold(seed): 0.170 Positive Predictive Value Sfold: 0.736 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Murlet(seed) Matthews Correlation Coefficient Sfold: 0.599 Murlet(seed): 0.468 Sensitivity Sfold: 0.552 Murlet(seed): 0.266 Positive Predictive Value Sfold: 0.654 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Alterna Matthews Correlation Coefficient Sfold: 0.603 Alterna: 0.552 Sensitivity Sfold: 0.566 Alterna: 0.547 Positive Predictive Value Sfold: 0.649 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Carnac(seed) Matthews Correlation Coefficient Sfold: 0.648 Carnac(seed): 0.415 Sensitivity Sfold: 0.608 Carnac(seed): 0.196 Positive Predictive Value Sfold: 0.695 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Vsfold4 Matthews Correlation Coefficient Sfold: 0.618 Vsfold4: 0.487 Sensitivity Sfold: 0.581 Vsfold4: 0.447 Positive Predictive Value Sfold: 0.663 Vsfold4: 0.537 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RSpredict(seed) Matthews Correlation Coefficient Sfold: 0.686 RSpredict(seed): 0.373 Sensitivity Sfold: 0.656 RSpredict(seed): 0.251 Positive Predictive Value Sfold: 0.721 RSpredict(seed): 0.562 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Vsfold5 Matthews Correlation Coefficient Sfold: 0.618 Vsfold5: 0.477 Sensitivity Sfold: 0.581 Vsfold5: 0.450 Positive Predictive Value Sfold: 0.663 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs RDfolder Matthews Correlation Coefficient Sfold: 0.603 RDfolder: 0.520 Sensitivity Sfold: 0.566 RDfolder: 0.464 Positive Predictive Value Sfold: 0.649 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs MCFold Matthews Correlation Coefficient Sfold: 0.621 MCFold: 0.473 Sensitivity Sfold: 0.583 MCFold: 0.524 Positive Predictive Value Sfold: 0.668 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs NanoFolder Matthews Correlation Coefficient Sfold: 0.631 NanoFolder: 0.335 Sensitivity Sfold: 0.600 NanoFolder: 0.384 Positive Predictive Value Sfold: 0.668 NanoFolder: 0.301 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Sfold vs Mastr(seed) Matthews Correlation Coefficient Sfold: 0.680 Mastr(seed): 0.263 Sensitivity Sfold: 0.648 Mastr(seed): 0.089 Positive Predictive Value Sfold: 0.718 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNAalifold(seed)	205 ContextFold vs RNAalifold(seed) Matthews Correlation Coefficient ContextFold: 0.836 RNAalifold(seed): 0.610 Sensitivity ContextFold: 0.809 RNAalifold(seed): 0.404 Positive Predictive Value ContextFold: 0.866 RNAalifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	137 TurboFold(20) vs RNAalifold(seed) Matthews Correlation Coefficient TurboFold(20): 0.829 RNAalifold(seed): 0.604 Sensitivity TurboFold(20): 0.810 RNAalifold(seed): 0.383 Positive Predictive Value TurboFold(20): 0.850 RNAalifold(seed): 0.956 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 3.56938820447e-08	205 CentroidAlifold(seed) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.802 RNAalifold(seed): 0.610 Sensitivity CentroidAlifold(seed): 0.719 RNAalifold(seed): 0.404 Positive Predictive Value CentroidAlifold(seed): 0.896 RNAalifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	205 CentroidHomfold‑LAST vs RNAalifold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.793 RNAalifold(seed): 0.610 Sensitivity CentroidHomfold‑LAST: 0.735 RNAalifold(seed): 0.404 Positive Predictive Value CentroidHomfold‑LAST: 0.858 RNAalifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	202 PETfold_pre2.0(seed) vs RNAalifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.737 RNAalifold(seed): 0.607 Sensitivity PETfold_pre2.0(seed): 0.639 RNAalifold(seed): 0.399 Positive Predictive Value PETfold_pre2.0(seed): 0.854 RNAalifold(seed): 0.927 Number of pairs reference - predicted secondary structure: 202 Wilcoxon single-rank test P-value: 3.56938820447e-08	32 TurboFold(seed) vs RNAalifold(seed) Matthews Correlation Coefficient TurboFold(seed): 0.790 RNAalifold(seed): 0.601 Sensitivity TurboFold(seed): 0.759 RNAalifold(seed): 0.408 Positive Predictive Value TurboFold(seed): 0.826 RNAalifold(seed): 0.890 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	205 MXScarna(seed) vs RNAalifold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.736 RNAalifold(seed): 0.610 Sensitivity MXScarna(seed): 0.697 RNAalifold(seed): 0.404 Positive Predictive Value MXScarna(seed): 0.780 RNAalifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	137 CentroidAlifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.694 RNAalifold(seed): 0.604 Sensitivity CentroidAlifold(20): 0.513 RNAalifold(seed): 0.383 Positive Predictive Value CentroidAlifold(20): 0.942 RNAalifold(seed): 0.956 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 3.56938820447e-08	137 PETfold_pre2.0(20) vs RNAalifold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.630 RNAalifold(seed): 0.604 Sensitivity PETfold_pre2.0(20): 0.426 RNAalifold(seed): 0.383 Positive Predictive Value PETfold_pre2.0(20): 0.935 RNAalifold(seed): 0.956 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 3.56938820447e-08	137 MXScarna(20) vs RNAalifold(seed) Matthews Correlation Coefficient MXScarna(20): 0.761 RNAalifold(seed): 0.604 Sensitivity MXScarna(20): 0.682 RNAalifold(seed): 0.383 Positive Predictive Value MXScarna(20): 0.852 RNAalifold(seed): 0.956 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 3.56938820447e-08	131 PPfold(20) vs RNAalifold(seed) Matthews Correlation Coefficient PPfold(20): 0.612 RNAalifold(seed): 0.607 Sensitivity PPfold(20): 0.400 RNAalifold(seed): 0.388 Positive Predictive Value PPfold(20): 0.941 RNAalifold(seed): 0.954 Number of pairs reference - predicted secondary structure: 131 Wilcoxon single-rank test P-value: 6.58294707158e-07	137 RNAalifold(20) vs RNAalifold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.630 RNAalifold(seed): 0.604 Sensitivity RNAalifold(20): 0.427 RNAalifold(seed): 0.383 Positive Predictive Value RNAalifold(20): 0.934 RNAalifold(seed): 0.956 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 3.56938820447e-08	137 RSpredict(20) vs RNAalifold(seed) Matthews Correlation Coefficient RSpredict(20): 0.710 RNAalifold(seed): 0.604 Sensitivity RSpredict(20): 0.586 RNAalifold(seed): 0.383 Positive Predictive Value RSpredict(20): 0.864 RNAalifold(seed): 0.956 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 3.56938820447e-08	205 IPknot vs RNAalifold(seed) Matthews Correlation Coefficient IPknot: 0.734 RNAalifold(seed): 0.610 Sensitivity IPknot: 0.708 RNAalifold(seed): 0.404 Positive Predictive Value IPknot: 0.764 RNAalifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	128 RNAalifold(seed) vs Multilign(20) Matthews Correlation Coefficient RNAalifold(seed): 0.612 Multilign(20): 0.583 Sensitivity RNAalifold(seed): 0.394 Multilign(20): 0.435 Positive Predictive Value RNAalifold(seed): 0.955 Multilign(20): 0.787 Number of pairs reference - predicted secondary structure: 128 Wilcoxon single-rank test P-value: 3.56938820447e-08	205 CentroidFold vs RNAalifold(seed) Matthews Correlation Coefficient CentroidFold: 0.698 RNAalifold(seed): 0.610 Sensitivity CentroidFold: 0.663 RNAalifold(seed): 0.404 Positive Predictive Value CentroidFold: 0.738 RNAalifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	205 Contrafold vs RNAalifold(seed) Matthews Correlation Coefficient Contrafold: 0.693 RNAalifold(seed): 0.610 Sensitivity Contrafold: 0.681 RNAalifold(seed): 0.404 Positive Predictive Value Contrafold: 0.709 RNAalifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	133 RNAalifold(seed) vs RNASampler(20) Matthews Correlation Coefficient RNAalifold(seed): 0.605 RNASampler(20): 0.591 Sensitivity RNAalifold(seed): 0.385 RNASampler(20): 0.378 Positive Predictive Value RNAalifold(seed): 0.954 RNASampler(20): 0.928 Number of pairs reference - predicted secondary structure: 133 Wilcoxon single-rank test P-value: 3.56938820447e-08	136 RNAalifold(seed) vs Murlet(20) Matthews Correlation Coefficient RNAalifold(seed): 0.603 Murlet(20): 0.601 Sensitivity RNAalifold(seed): 0.381 Murlet(20): 0.392 Positive Predictive Value RNAalifold(seed): 0.959 Murlet(20): 0.924 Number of pairs reference - predicted secondary structure: 136 Wilcoxon single-rank test P-value: 6.93152570412e-05	78 RNAalifold(seed) vs CMfinder(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.654 CMfinder(seed): 0.571 Sensitivity RNAalifold(seed): 0.499 CMfinder(seed): 0.439 Positive Predictive Value RNAalifold(seed): 0.860 CMfinder(seed): 0.747 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	205 MaxExpect vs RNAalifold(seed) Matthews Correlation Coefficient MaxExpect: 0.695 RNAalifold(seed): 0.610 Sensitivity MaxExpect: 0.684 RNAalifold(seed): 0.404 Positive Predictive Value MaxExpect: 0.710 RNAalifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	133 CMfinder(20) vs RNAalifold(seed) Matthews Correlation Coefficient CMfinder(20): 0.642 RNAalifold(seed): 0.608 Sensitivity CMfinder(20): 0.492 RNAalifold(seed): 0.389 Positive Predictive Value CMfinder(20): 0.844 RNAalifold(seed): 0.954 Number of pairs reference - predicted secondary structure: 133 Wilcoxon single-rank test P-value: 3.56938820447e-08	205 CRWrnafold vs RNAalifold(seed) Matthews Correlation Coefficient CRWrnafold: 0.711 RNAalifold(seed): 0.610 Sensitivity CRWrnafold: 0.701 RNAalifold(seed): 0.404 Positive Predictive Value CRWrnafold: 0.724 RNAalifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	205 ProbKnot vs RNAalifold(seed) Matthews Correlation Coefficient ProbKnot: 0.689 RNAalifold(seed): 0.610 Sensitivity ProbKnot: 0.680 RNAalifold(seed): 0.404 Positive Predictive Value ProbKnot: 0.701 RNAalifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	137 Mastr(20) vs RNAalifold(seed) Matthews Correlation Coefficient Mastr(20): 0.650 RNAalifold(seed): 0.604 Sensitivity Mastr(20): 0.509 RNAalifold(seed): 0.383 Positive Predictive Value Mastr(20): 0.834 RNAalifold(seed): 0.956 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 3.56938820447e-08	205 Fold vs RNAalifold(seed) Matthews Correlation Coefficient Fold: 0.705 RNAalifold(seed): 0.610 Sensitivity Fold: 0.702 RNAalifold(seed): 0.404 Positive Predictive Value Fold: 0.712 RNAalifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	205 UNAFold vs RNAalifold(seed) Matthews Correlation Coefficient UNAFold: 0.711 RNAalifold(seed): 0.610 Sensitivity UNAFold: 0.701 RNAalifold(seed): 0.404 Positive Predictive Value UNAFold: 0.724 RNAalifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	205 PknotsRG vs RNAalifold(seed) Matthews Correlation Coefficient PknotsRG: 0.714 RNAalifold(seed): 0.610 Sensitivity PknotsRG: 0.711 RNAalifold(seed): 0.404 Positive Predictive Value PknotsRG: 0.720 RNAalifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	205 Sfold vs RNAalifold(seed) Matthews Correlation Coefficient Sfold: 0.690 RNAalifold(seed): 0.610 Sensitivity Sfold: 0.658 RNAalifold(seed): 0.404 Positive Predictive Value Sfold: 0.727 RNAalifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08		- RNAsubopt vs RNAalifold(seed) Matthews Correlation Coefficient RNAsubopt: 0.657 RNAalifold(seed): 0.610 Sensitivity RNAsubopt: 0.655 RNAalifold(seed): 0.404 Positive Predictive Value RNAsubopt: 0.663 RNAalifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	- HotKnots vs RNAalifold(seed) Matthews Correlation Coefficient HotKnots: 0.696 RNAalifold(seed): 0.602 Sensitivity HotKnots: 0.695 RNAalifold(seed): 0.395 Positive Predictive Value HotKnots: 0.701 RNAalifold(seed): 0.920 Number of pairs reference - predicted secondary structure: 201 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNAfold vs RNAalifold(seed) Matthews Correlation Coefficient RNAfold: 0.701 RNAalifold(seed): 0.610 Sensitivity RNAfold: 0.695 RNAalifold(seed): 0.404 Positive Predictive Value RNAfold: 0.710 RNAalifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNAshapes vs RNAalifold(seed) Matthews Correlation Coefficient RNAshapes: 0.686 RNAalifold(seed): 0.610 Sensitivity RNAshapes: 0.681 RNAalifold(seed): 0.404 Positive Predictive Value RNAshapes: 0.695 RNAalifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs RNASampler(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.657 RNASampler(seed): 0.557 Sensitivity RNAalifold(seed): 0.501 RNASampler(seed): 0.389 Positive Predictive Value RNAalifold(seed): 0.865 RNASampler(seed): 0.802 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Afold vs RNAalifold(seed) Matthews Correlation Coefficient Afold: 0.649 RNAalifold(seed): 0.626 Sensitivity Afold: 0.646 RNAalifold(seed): 0.424 Positive Predictive Value Afold: 0.657 RNAalifold(seed): 0.927 Number of pairs reference - predicted secondary structure: 162 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Pknots Matthews Correlation Coefficient RNAalifold(seed): 0.618 Pknots: 0.488 Sensitivity RNAalifold(seed): 0.420 Pknots: 0.481 Positive Predictive Value RNAalifold(seed): 0.914 Pknots: 0.503 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs McQFold Matthews Correlation Coefficient RNAalifold(seed): 0.610 McQFold: 0.550 Sensitivity RNAalifold(seed): 0.404 McQFold: 0.524 Positive Predictive Value RNAalifold(seed): 0.923 McQFold: 0.583 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(seed): 0.604 Carnac(20): 0.455 Sensitivity RNAalifold(seed): 0.383 Carnac(20): 0.248 Positive Predictive Value RNAalifold(seed): 0.956 Carnac(20): 0.840 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(seed): 0.610 RNASLOpt: 0.572 Sensitivity RNAalifold(seed): 0.404 RNASLOpt: 0.521 Positive Predictive Value RNAalifold(seed): 0.923 RNASLOpt: 0.632 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Cylofold Matthews Correlation Coefficient RNAalifold(seed): 0.578 Cylofold: 0.512 Sensitivity RNAalifold(seed): 0.370 Cylofold: 0.484 Positive Predictive Value RNAalifold(seed): 0.909 Cylofold: 0.548 Number of pairs reference - predicted secondary structure: 187 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Multilign(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.590 Multilign(seed): 0.485 Sensitivity RNAalifold(seed): 0.447 Multilign(seed): 0.386 Positive Predictive Value RNAalifold(seed): 0.787 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.45096400029e-08	+ RNAalifold(seed) vs RNAwolf Matthews Correlation Coefficient RNAalifold(seed): 0.610 RNAwolf: 0.529 Sensitivity RNAalifold(seed): 0.404 RNAwolf: 0.534 Positive Predictive Value RNAalifold(seed): 0.923 RNAwolf: 0.531 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs PPfold(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.588 PPfold(seed): 0.425 Sensitivity RNAalifold(seed): 0.386 PPfold(seed): 0.213 Positive Predictive Value RNAalifold(seed): 0.901 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.644 Murlet(seed): 0.468 Sensitivity RNAalifold(seed): 0.479 Murlet(seed): 0.266 Positive Predictive Value RNAalifold(seed): 0.871 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Alterna Matthews Correlation Coefficient RNAalifold(seed): 0.617 Alterna: 0.554 Sensitivity RNAalifold(seed): 0.418 Alterna: 0.541 Positive Predictive Value RNAalifold(seed): 0.917 Alterna: 0.575 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.643 Carnac(seed): 0.439 Sensitivity RNAalifold(seed): 0.466 Carnac(seed): 0.219 Positive Predictive Value RNAalifold(seed): 0.892 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 112 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(seed): 0.610 Vsfold4: 0.338 Sensitivity RNAalifold(seed): 0.404 Vsfold4: 0.307 Positive Predictive Value RNAalifold(seed): 0.923 Vsfold4: 0.379 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.610 RSpredict(seed): 0.385 Sensitivity RNAalifold(seed): 0.404 RSpredict(seed): 0.262 Positive Predictive Value RNAalifold(seed): 0.923 RSpredict(seed): 0.571 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(seed): 0.610 Vsfold5: 0.291 Sensitivity RNAalifold(seed): 0.404 Vsfold5: 0.271 Positive Predictive Value RNAalifold(seed): 0.923 Vsfold5: 0.321 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs RDfolder Matthews Correlation Coefficient RNAalifold(seed): 0.617 RDfolder: 0.448 Sensitivity RNAalifold(seed): 0.418 RDfolder: 0.382 Positive Predictive Value RNAalifold(seed): 0.917 RDfolder: 0.533 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs MCFold Matthews Correlation Coefficient RNAalifold(seed): 0.612 MCFold: 0.476 Sensitivity RNAalifold(seed): 0.404 MCFold: 0.525 Positive Predictive Value RNAalifold(seed): 0.932 MCFold: 0.438 Number of pairs reference - predicted secondary structure: 175 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs NanoFolder Matthews Correlation Coefficient RNAalifold(seed): 0.600 NanoFolder: 0.391 Sensitivity RNAalifold(seed): 0.377 NanoFolder: 0.446 Positive Predictive Value RNAalifold(seed): 0.960 NanoFolder: 0.350 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAalifold(seed) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.610 Mastr(seed): 0.282 Sensitivity RNAalifold(seed): 0.404 Mastr(seed): 0.102 Positive Predictive Value RNAalifold(seed): 0.923 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNAsubopt	882 ContextFold vs RNAsubopt Matthews Correlation Coefficient ContextFold: 0.779 RNAsubopt: 0.615 Sensitivity ContextFold: 0.741 RNAsubopt: 0.609 Positive Predictive Value ContextFold: 0.823 RNAsubopt: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 TurboFold(20) vs RNAsubopt Matthews Correlation Coefficient TurboFold(20): 0.889 RNAsubopt: 0.694 Sensitivity TurboFold(20): 0.861 RNAsubopt: 0.693 Positive Predictive Value TurboFold(20): 0.919 RNAsubopt: 0.700 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	216 CentroidAlifold(seed) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(seed): 0.790 RNAsubopt: 0.655 Sensitivity CentroidAlifold(seed): 0.699 RNAsubopt: 0.654 Positive Predictive Value CentroidAlifold(seed): 0.896 RNAsubopt: 0.660 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 CentroidHomfold‑LAST vs RNAsubopt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.736 RNAsubopt: 0.615 Sensitivity CentroidHomfold‑LAST: 0.665 RNAsubopt: 0.609 Positive Predictive Value CentroidHomfold‑LAST: 0.818 RNAsubopt: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	498 PETfold_pre2.0(seed) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.879 RNAsubopt: 0.667 Sensitivity PETfold_pre2.0(seed): 0.825 RNAsubopt: 0.670 Positive Predictive Value PETfold_pre2.0(seed): 0.938 RNAsubopt: 0.668 Number of pairs reference - predicted secondary structure: 498 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 TurboFold(seed) vs RNAsubopt Matthews Correlation Coefficient TurboFold(seed): 0.798 RNAsubopt: 0.730 Sensitivity TurboFold(seed): 0.766 RNAsubopt: 0.721 Positive Predictive Value TurboFold(seed): 0.835 RNAsubopt: 0.744 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	233 MXScarna(seed) vs RNAsubopt Matthews Correlation Coefficient MXScarna(seed): 0.750 RNAsubopt: 0.652 Sensitivity MXScarna(seed): 0.712 RNAsubopt: 0.651 Positive Predictive Value MXScarna(seed): 0.793 RNAsubopt: 0.656 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 CentroidAlifold(20) vs RNAsubopt Matthews Correlation Coefficient CentroidAlifold(20): 0.849 RNAsubopt: 0.694 Sensitivity CentroidAlifold(20): 0.754 RNAsubopt: 0.693 Positive Predictive Value CentroidAlifold(20): 0.957 RNAsubopt: 0.700 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 PETfold_pre2.0(20) vs RNAsubopt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 RNAsubopt: 0.694 Sensitivity PETfold_pre2.0(20): 0.737 RNAsubopt: 0.693 Positive Predictive Value PETfold_pre2.0(20): 0.975 RNAsubopt: 0.700 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 MXScarna(20) vs RNAsubopt Matthews Correlation Coefficient MXScarna(20): 0.838 RNAsubopt: 0.694 Sensitivity MXScarna(20): 0.791 RNAsubopt: 0.693 Positive Predictive Value MXScarna(20): 0.891 RNAsubopt: 0.700 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	314 PPfold(20) vs RNAsubopt Matthews Correlation Coefficient PPfold(20): 0.839 RNAsubopt: 0.693 Sensitivity PPfold(20): 0.721 RNAsubopt: 0.691 Positive Predictive Value PPfold(20): 0.977 RNAsubopt: 0.699 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RNAalifold(20) vs RNAsubopt Matthews Correlation Coefficient RNAalifold(20): 0.816 RNAsubopt: 0.694 Sensitivity RNAalifold(20): 0.690 RNAsubopt: 0.693 Positive Predictive Value RNAalifold(20): 0.966 RNAsubopt: 0.700 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RSpredict(20) vs RNAsubopt Matthews Correlation Coefficient RSpredict(20): 0.789 RNAsubopt: 0.694 Sensitivity RSpredict(20): 0.693 RNAsubopt: 0.693 Positive Predictive Value RSpredict(20): 0.901 RNAsubopt: 0.700 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 IPknot vs RNAsubopt Matthews Correlation Coefficient IPknot: 0.694 RNAsubopt: 0.615 Sensitivity IPknot: 0.661 RNAsubopt: 0.609 Positive Predictive Value IPknot: 0.733 RNAsubopt: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	311 Multilign(20) vs RNAsubopt Matthews Correlation Coefficient Multilign(20): 0.784 RNAsubopt: 0.694 Sensitivity Multilign(20): 0.697 RNAsubopt: 0.693 Positive Predictive Value Multilign(20): 0.885 RNAsubopt: 0.699 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 CentroidFold vs RNAsubopt Matthews Correlation Coefficient CentroidFold: 0.645 RNAsubopt: 0.615 Sensitivity CentroidFold: 0.612 RNAsubopt: 0.609 Positive Predictive Value CentroidFold: 0.684 RNAsubopt: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 Contrafold vs RNAsubopt Matthews Correlation Coefficient Contrafold: 0.643 RNAsubopt: 0.615 Sensitivity Contrafold: 0.634 RNAsubopt: 0.609 Positive Predictive Value Contrafold: 0.657 RNAsubopt: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	315 RNASampler(20) vs RNAsubopt Matthews Correlation Coefficient RNASampler(20): 0.770 RNAsubopt: 0.697 Sensitivity RNASampler(20): 0.622 RNAsubopt: 0.695 Positive Predictive Value RNASampler(20): 0.957 RNAsubopt: 0.703 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	319 Murlet(20) vs RNAsubopt Matthews Correlation Coefficient Murlet(20): 0.750 RNAsubopt: 0.695 Sensitivity Murlet(20): 0.619 RNAsubopt: 0.694 Positive Predictive Value Murlet(20): 0.913 RNAsubopt: 0.700 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 CMfinder(seed) vs RNAsubopt Matthews Correlation Coefficient CMfinder(seed): 0.571 RNAsubopt: 0.527 Sensitivity CMfinder(seed): 0.439 RNAsubopt: 0.511 Positive Predictive Value CMfinder(seed): 0.747 RNAsubopt: 0.549 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 MaxExpect vs RNAsubopt Matthews Correlation Coefficient MaxExpect: 0.633 RNAsubopt: 0.615 Sensitivity MaxExpect: 0.617 RNAsubopt: 0.609 Positive Predictive Value MaxExpect: 0.654 RNAsubopt: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	316 CMfinder(20) vs RNAsubopt Matthews Correlation Coefficient CMfinder(20): 0.735 RNAsubopt: 0.692 Sensitivity CMfinder(20): 0.603 RNAsubopt: 0.691 Positive Predictive Value CMfinder(20): 0.899 RNAsubopt: 0.697 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	881 CRWrnafold vs RNAsubopt Matthews Correlation Coefficient CRWrnafold: 0.630 RNAsubopt: 0.615 Sensitivity CRWrnafold: 0.618 RNAsubopt: 0.609 Positive Predictive Value CRWrnafold: 0.648 RNAsubopt: 0.626 Number of pairs reference - predicted secondary structure: 881 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 ProbKnot vs RNAsubopt Matthews Correlation Coefficient ProbKnot: 0.630 RNAsubopt: 0.615 Sensitivity ProbKnot: 0.622 RNAsubopt: 0.609 Positive Predictive Value ProbKnot: 0.644 RNAsubopt: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 Mastr(20) vs RNAsubopt Matthews Correlation Coefficient Mastr(20): 0.708 RNAsubopt: 0.694 Sensitivity Mastr(20): 0.635 RNAsubopt: 0.693 Positive Predictive Value Mastr(20): 0.793 RNAsubopt: 0.700 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 4.48494289621e-08	882 Fold vs RNAsubopt Matthews Correlation Coefficient Fold: 0.628 RNAsubopt: 0.615 Sensitivity Fold: 0.620 RNAsubopt: 0.609 Positive Predictive Value Fold: 0.641 RNAsubopt: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 UNAFold vs RNAsubopt Matthews Correlation Coefficient UNAFold: 0.620 RNAsubopt: 0.615 Sensitivity UNAFold: 0.605 RNAsubopt: 0.609 Positive Predictive Value UNAFold: 0.639 RNAsubopt: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 5.62644058675e-08	882 PknotsRG vs RNAsubopt Matthews Correlation Coefficient PknotsRG: 0.617 RNAsubopt: 0.615 Sensitivity PknotsRG: 0.610 RNAsubopt: 0.609 Positive Predictive Value PknotsRG: 0.630 RNAsubopt: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.76761760679e-06	882 Sfold vs RNAsubopt Matthews Correlation Coefficient Sfold: 0.618 RNAsubopt: 0.615 Sensitivity Sfold: 0.581 RNAsubopt: 0.609 Positive Predictive Value Sfold: 0.663 RNAsubopt: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.85233844192e-08	205 RNAsubopt vs RNAalifold(seed) Matthews Correlation Coefficient RNAsubopt: 0.657 RNAalifold(seed): 0.610 Sensitivity RNAsubopt: 0.655 RNAalifold(seed): 0.404 Positive Predictive Value RNAsubopt: 0.663 RNAalifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ RNAsubopt vs HotKnots Matthews Correlation Coefficient RNAsubopt: 0.615 HotKnots: 0.613 Sensitivity RNAsubopt: 0.609 HotKnots: 0.607 Positive Predictive Value RNAsubopt: 0.627 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 875 Wilcoxon single-rank test P-value: 8.62431444312e-06	+ RNAsubopt vs RNAfold Matthews Correlation Coefficient RNAsubopt: 0.615 RNAfold: 0.612 Sensitivity RNAsubopt: 0.609 RNAfold: 0.604 Positive Predictive Value RNAsubopt: 0.626 RNAfold: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 4.1569883686e-08	+ RNAsubopt vs RNAshapes Matthews Correlation Coefficient RNAsubopt: 0.615 RNAshapes: 0.612 Sensitivity RNAsubopt: 0.609 RNAshapes: 0.602 Positive Predictive Value RNAsubopt: 0.626 RNAshapes: 0.628 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 8.1815824276e-08	- RNASampler(seed) vs RNAsubopt Matthews Correlation Coefficient RNASampler(seed): 0.557 RNAsubopt: 0.547 Sensitivity RNASampler(seed): 0.389 RNAsubopt: 0.529 Positive Predictive Value RNASampler(seed): 0.802 RNAsubopt: 0.570 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 6.58294707158e-07	+ RNAsubopt vs Afold Matthews Correlation Coefficient RNAsubopt: 0.604 Afold: 0.558 Sensitivity RNAsubopt: 0.586 Afold: 0.541 Positive Predictive Value RNAsubopt: 0.629 Afold: 0.582 Number of pairs reference - predicted secondary structure: 530 Wilcoxon single-rank test P-value: 3.56938820447e-08	= RNAsubopt vs Pknots Matthews Correlation Coefficient RNAsubopt: 0.608 Pknots: 0.606 Sensitivity RNAsubopt: 0.602 Pknots: 0.595 Positive Predictive Value RNAsubopt: 0.620 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 0.00297289556633	+ RNAsubopt vs McQFold Matthews Correlation Coefficient RNAsubopt: 0.615 McQFold: 0.583 Sensitivity RNAsubopt: 0.609 McQFold: 0.557 Positive Predictive Value RNAsubopt: 0.626 McQFold: 0.616 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Carnac(20) Matthews Correlation Coefficient RNAsubopt: 0.694 Carnac(20): 0.675 Sensitivity RNAsubopt: 0.693 Carnac(20): 0.500 Positive Predictive Value RNAsubopt: 0.700 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs RNASLOpt Matthews Correlation Coefficient RNAsubopt: 0.615 RNASLOpt: 0.562 Sensitivity RNAsubopt: 0.609 RNASLOpt: 0.521 Positive Predictive Value RNAsubopt: 0.626 RNASLOpt: 0.613 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Cylofold Matthews Correlation Coefficient RNAsubopt: 0.641 Cylofold: 0.577 Sensitivity RNAsubopt: 0.633 Cylofold: 0.554 Positive Predictive Value RNAsubopt: 0.654 Cylofold: 0.608 Number of pairs reference - predicted secondary structure: 796 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Multilign(seed) vs RNAsubopt Matthews Correlation Coefficient Multilign(seed): 0.485 RNAsubopt: 0.465 Sensitivity Multilign(seed): 0.386 RNAsubopt: 0.437 Positive Predictive Value Multilign(seed): 0.619 RNAsubopt: 0.505 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 9.94451398341e-06	+ RNAsubopt vs RNAwolf Matthews Correlation Coefficient RNAsubopt: 0.615 RNAwolf: 0.518 Sensitivity RNAsubopt: 0.609 RNAwolf: 0.523 Positive Predictive Value RNAsubopt: 0.626 RNAwolf: 0.520 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs PPfold(seed) Matthews Correlation Coefficient RNAsubopt: 0.721 PPfold(seed): 0.380 Sensitivity RNAsubopt: 0.720 PPfold(seed): 0.170 Positive Predictive Value RNAsubopt: 0.727 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Murlet(seed) Matthews Correlation Coefficient RNAsubopt: 0.579 Murlet(seed): 0.468 Sensitivity RNAsubopt: 0.563 Murlet(seed): 0.266 Positive Predictive Value RNAsubopt: 0.601 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Alterna Matthews Correlation Coefficient RNAsubopt: 0.608 Alterna: 0.552 Sensitivity RNAsubopt: 0.603 Alterna: 0.547 Positive Predictive Value RNAsubopt: 0.621 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Carnac(seed) Matthews Correlation Coefficient RNAsubopt: 0.635 Carnac(seed): 0.415 Sensitivity RNAsubopt: 0.625 Carnac(seed): 0.196 Positive Predictive Value RNAsubopt: 0.649 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Vsfold4 Matthews Correlation Coefficient RNAsubopt: 0.615 Vsfold4: 0.487 Sensitivity RNAsubopt: 0.609 Vsfold4: 0.447 Positive Predictive Value RNAsubopt: 0.626 Vsfold4: 0.537 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs RSpredict(seed) Matthews Correlation Coefficient RNAsubopt: 0.655 RSpredict(seed): 0.373 Sensitivity RNAsubopt: 0.654 RSpredict(seed): 0.251 Positive Predictive Value RNAsubopt: 0.660 RSpredict(seed): 0.562 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Vsfold5 Matthews Correlation Coefficient RNAsubopt: 0.615 Vsfold5: 0.477 Sensitivity RNAsubopt: 0.609 Vsfold5: 0.450 Positive Predictive Value RNAsubopt: 0.626 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs RDfolder Matthews Correlation Coefficient RNAsubopt: 0.608 RDfolder: 0.520 Sensitivity RNAsubopt: 0.603 RDfolder: 0.464 Positive Predictive Value RNAsubopt: 0.621 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs MCFold Matthews Correlation Coefficient RNAsubopt: 0.619 MCFold: 0.473 Sensitivity RNAsubopt: 0.610 MCFold: 0.524 Positive Predictive Value RNAsubopt: 0.633 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs NanoFolder Matthews Correlation Coefficient RNAsubopt: 0.640 NanoFolder: 0.335 Sensitivity RNAsubopt: 0.632 NanoFolder: 0.384 Positive Predictive Value RNAsubopt: 0.652 NanoFolder: 0.301 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAsubopt vs Mastr(seed) Matthews Correlation Coefficient RNAsubopt: 0.652 Mastr(seed): 0.263 Sensitivity RNAsubopt: 0.651 Mastr(seed): 0.089 Positive Predictive Value RNAsubopt: 0.656 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08
HotKnots	875 ContextFold vs HotKnots Matthews Correlation Coefficient ContextFold: 0.779 HotKnots: 0.613 Sensitivity ContextFold: 0.740 HotKnots: 0.607 Positive Predictive Value ContextFold: 0.822 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 875 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 TurboFold(20) vs HotKnots Matthews Correlation Coefficient TurboFold(20): 0.889 HotKnots: 0.698 Sensitivity TurboFold(20): 0.861 HotKnots: 0.695 Positive Predictive Value TurboFold(20): 0.919 HotKnots: 0.705 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	212 CentroidAlifold(seed) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(seed): 0.788 HotKnots: 0.688 Sensitivity CentroidAlifold(seed): 0.697 HotKnots: 0.689 Positive Predictive Value CentroidAlifold(seed): 0.894 HotKnots: 0.691 Number of pairs reference - predicted secondary structure: 212 Wilcoxon single-rank test P-value: 3.56938820447e-08	875 CentroidHomfold‑LAST vs HotKnots Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.735 HotKnots: 0.613 Sensitivity CentroidHomfold‑LAST: 0.666 HotKnots: 0.607 Positive Predictive Value CentroidHomfold‑LAST: 0.816 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 875 Wilcoxon single-rank test P-value: 3.56938820447e-08	494 PETfold_pre2.0(seed) vs HotKnots Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.879 HotKnots: 0.657 Sensitivity PETfold_pre2.0(seed): 0.826 HotKnots: 0.660 Positive Predictive Value PETfold_pre2.0(seed): 0.938 HotKnots: 0.659 Number of pairs reference - predicted secondary structure: 494 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 TurboFold(seed) vs HotKnots Matthews Correlation Coefficient TurboFold(seed): 0.798 HotKnots: 0.740 Sensitivity TurboFold(seed): 0.766 HotKnots: 0.745 Positive Predictive Value TurboFold(seed): 0.835 HotKnots: 0.740 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 5.23657817852e-08	229 MXScarna(seed) vs HotKnots Matthews Correlation Coefficient MXScarna(seed): 0.754 HotKnots: 0.677 Sensitivity MXScarna(seed): 0.718 HotKnots: 0.678 Positive Predictive Value MXScarna(seed): 0.796 HotKnots: 0.680 Number of pairs reference - predicted secondary structure: 229 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 CentroidAlifold(20) vs HotKnots Matthews Correlation Coefficient CentroidAlifold(20): 0.849 HotKnots: 0.698 Sensitivity CentroidAlifold(20): 0.754 HotKnots: 0.695 Positive Predictive Value CentroidAlifold(20): 0.957 HotKnots: 0.705 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 PETfold_pre2.0(20) vs HotKnots Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 HotKnots: 0.698 Sensitivity PETfold_pre2.0(20): 0.737 HotKnots: 0.695 Positive Predictive Value PETfold_pre2.0(20): 0.975 HotKnots: 0.705 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 MXScarna(20) vs HotKnots Matthews Correlation Coefficient MXScarna(20): 0.838 HotKnots: 0.698 Sensitivity MXScarna(20): 0.791 HotKnots: 0.695 Positive Predictive Value MXScarna(20): 0.891 HotKnots: 0.705 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	314 PPfold(20) vs HotKnots Matthews Correlation Coefficient PPfold(20): 0.839 HotKnots: 0.696 Sensitivity PPfold(20): 0.721 HotKnots: 0.692 Positive Predictive Value PPfold(20): 0.977 HotKnots: 0.704 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RNAalifold(20) vs HotKnots Matthews Correlation Coefficient RNAalifold(20): 0.816 HotKnots: 0.698 Sensitivity RNAalifold(20): 0.690 HotKnots: 0.695 Positive Predictive Value RNAalifold(20): 0.966 HotKnots: 0.705 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RSpredict(20) vs HotKnots Matthews Correlation Coefficient RSpredict(20): 0.789 HotKnots: 0.698 Sensitivity RSpredict(20): 0.693 HotKnots: 0.695 Positive Predictive Value RSpredict(20): 0.901 HotKnots: 0.705 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	875 IPknot vs HotKnots Matthews Correlation Coefficient IPknot: 0.692 HotKnots: 0.613 Sensitivity IPknot: 0.659 HotKnots: 0.607 Positive Predictive Value IPknot: 0.730 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 875 Wilcoxon single-rank test P-value: 3.56938820447e-08	311 Multilign(20) vs HotKnots Matthews Correlation Coefficient Multilign(20): 0.784 HotKnots: 0.696 Sensitivity Multilign(20): 0.697 HotKnots: 0.692 Positive Predictive Value Multilign(20): 0.885 HotKnots: 0.703 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	875 CentroidFold vs HotKnots Matthews Correlation Coefficient CentroidFold: 0.645 HotKnots: 0.613 Sensitivity CentroidFold: 0.612 HotKnots: 0.607 Positive Predictive Value CentroidFold: 0.684 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 875 Wilcoxon single-rank test P-value: 3.56938820447e-08	875 Contrafold vs HotKnots Matthews Correlation Coefficient Contrafold: 0.643 HotKnots: 0.613 Sensitivity Contrafold: 0.635 HotKnots: 0.607 Positive Predictive Value Contrafold: 0.657 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 875 Wilcoxon single-rank test P-value: 3.56938820447e-08	315 RNASampler(20) vs HotKnots Matthews Correlation Coefficient RNASampler(20): 0.770 HotKnots: 0.698 Sensitivity RNASampler(20): 0.622 HotKnots: 0.694 Positive Predictive Value RNASampler(20): 0.957 HotKnots: 0.706 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	319 Murlet(20) vs HotKnots Matthews Correlation Coefficient Murlet(20): 0.750 HotKnots: 0.699 Sensitivity Murlet(20): 0.619 HotKnots: 0.696 Positive Predictive Value Murlet(20): 0.913 HotKnots: 0.706 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	75 CMfinder(seed) vs HotKnots Matthews Correlation Coefficient CMfinder(seed): 0.593 HotKnots: 0.499 Sensitivity CMfinder(seed): 0.459 HotKnots: 0.488 Positive Predictive Value CMfinder(seed): 0.771 HotKnots: 0.517 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 3.56938820447e-08	875 MaxExpect vs HotKnots Matthews Correlation Coefficient MaxExpect: 0.634 HotKnots: 0.613 Sensitivity MaxExpect: 0.618 HotKnots: 0.607 Positive Predictive Value MaxExpect: 0.656 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 875 Wilcoxon single-rank test P-value: 3.56938820447e-08	316 CMfinder(20) vs HotKnots Matthews Correlation Coefficient CMfinder(20): 0.735 HotKnots: 0.696 Sensitivity CMfinder(20): 0.603 HotKnots: 0.693 Positive Predictive Value CMfinder(20): 0.899 HotKnots: 0.703 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	874 CRWrnafold vs HotKnots Matthews Correlation Coefficient CRWrnafold: 0.632 HotKnots: 0.613 Sensitivity CRWrnafold: 0.620 HotKnots: 0.607 Positive Predictive Value CRWrnafold: 0.650 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 874 Wilcoxon single-rank test P-value: 3.56938820447e-08	875 ProbKnot vs HotKnots Matthews Correlation Coefficient ProbKnot: 0.632 HotKnots: 0.613 Sensitivity ProbKnot: 0.623 HotKnots: 0.607 Positive Predictive Value ProbKnot: 0.646 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 875 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 Mastr(20) vs HotKnots Matthews Correlation Coefficient Mastr(20): 0.708 HotKnots: 0.698 Sensitivity Mastr(20): 0.635 HotKnots: 0.695 Positive Predictive Value Mastr(20): 0.793 HotKnots: 0.705 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 4.48494289621e-08	875 Fold vs HotKnots Matthews Correlation Coefficient Fold: 0.630 HotKnots: 0.613 Sensitivity Fold: 0.622 HotKnots: 0.607 Positive Predictive Value Fold: 0.643 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 875 Wilcoxon single-rank test P-value: 3.56938820447e-08	875 UNAFold vs HotKnots Matthews Correlation Coefficient UNAFold: 0.618 HotKnots: 0.613 Sensitivity UNAFold: 0.603 HotKnots: 0.607 Positive Predictive Value UNAFold: 0.638 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 875 Wilcoxon single-rank test P-value: 3.56938820447e-08	875 PknotsRG vs HotKnots Matthews Correlation Coefficient PknotsRG: 0.617 HotKnots: 0.613 Sensitivity PknotsRG: 0.610 HotKnots: 0.607 Positive Predictive Value PknotsRG: 0.630 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 875 Wilcoxon single-rank test P-value: 3.85233844192e-08	875 Sfold vs HotKnots Matthews Correlation Coefficient Sfold: 0.617 HotKnots: 0.613 Sensitivity Sfold: 0.581 HotKnots: 0.607 Positive Predictive Value Sfold: 0.662 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 875 Wilcoxon single-rank test P-value: 3.56938820447e-08	201 HotKnots vs RNAalifold(seed) Matthews Correlation Coefficient HotKnots: 0.696 RNAalifold(seed): 0.602 Sensitivity HotKnots: 0.695 RNAalifold(seed): 0.395 Positive Predictive Value HotKnots: 0.701 RNAalifold(seed): 0.920 Number of pairs reference - predicted secondary structure: 201 Wilcoxon single-rank test P-value: 3.56938820447e-08	875 RNAsubopt vs HotKnots Matthews Correlation Coefficient RNAsubopt: 0.615 HotKnots: 0.613 Sensitivity RNAsubopt: 0.609 HotKnots: 0.607 Positive Predictive Value RNAsubopt: 0.627 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 875 Wilcoxon single-rank test P-value: 8.62431444312e-06		+ HotKnots vs RNAfold Matthews Correlation Coefficient HotKnots: 0.613 RNAfold: 0.612 Sensitivity HotKnots: 0.607 RNAfold: 0.604 Positive Predictive Value HotKnots: 0.624 RNAfold: 0.626 Number of pairs reference - predicted secondary structure: 875 Wilcoxon single-rank test P-value: 0.000230581642477	= RNAshapes vs HotKnots Matthews Correlation Coefficient RNAshapes: 0.613 HotKnots: 0.613 Sensitivity RNAshapes: 0.603 HotKnots: 0.607 Positive Predictive Value RNAshapes: 0.628 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 875 Wilcoxon single-rank test P-value: 0.0738256256282	= RNASampler(seed) vs HotKnots Matthews Correlation Coefficient RNASampler(seed): 0.538 HotKnots: 0.533 Sensitivity RNASampler(seed): 0.371 HotKnots: 0.522 Positive Predictive Value RNASampler(seed): 0.786 HotKnots: 0.550 Number of pairs reference - predicted secondary structure: 83 Wilcoxon single-rank test P-value: 0.00842627253913	+ HotKnots vs Afold Matthews Correlation Coefficient HotKnots: 0.623 Afold: 0.559 Sensitivity HotKnots: 0.603 Afold: 0.541 Positive Predictive Value HotKnots: 0.650 Afold: 0.583 Number of pairs reference - predicted secondary structure: 526 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Pknots vs HotKnots Matthews Correlation Coefficient Pknots: 0.606 HotKnots: 0.593 Sensitivity Pknots: 0.595 HotKnots: 0.589 Positive Predictive Value Pknots: 0.624 HotKnots: 0.604 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs McQFold Matthews Correlation Coefficient HotKnots: 0.613 McQFold: 0.583 Sensitivity HotKnots: 0.607 McQFold: 0.558 Positive Predictive Value HotKnots: 0.624 McQFold: 0.616 Number of pairs reference - predicted secondary structure: 875 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Carnac(20) Matthews Correlation Coefficient HotKnots: 0.698 Carnac(20): 0.675 Sensitivity HotKnots: 0.695 Carnac(20): 0.500 Positive Predictive Value HotKnots: 0.705 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs RNASLOpt Matthews Correlation Coefficient HotKnots: 0.613 RNASLOpt: 0.562 Sensitivity HotKnots: 0.607 RNASLOpt: 0.520 Positive Predictive Value HotKnots: 0.624 RNASLOpt: 0.613 Number of pairs reference - predicted secondary structure: 875 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Cylofold Matthews Correlation Coefficient HotKnots: 0.638 Cylofold: 0.577 Sensitivity HotKnots: 0.631 Cylofold: 0.554 Positive Predictive Value HotKnots: 0.651 Cylofold: 0.608 Number of pairs reference - predicted secondary structure: 796 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Multilign(seed) Matthews Correlation Coefficient HotKnots: 0.519 Multilign(seed): 0.485 Sensitivity HotKnots: 0.521 Multilign(seed): 0.386 Positive Predictive Value HotKnots: 0.526 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 4.52862048029e-08	+ HotKnots vs RNAwolf Matthews Correlation Coefficient HotKnots: 0.613 RNAwolf: 0.518 Sensitivity HotKnots: 0.607 RNAwolf: 0.523 Positive Predictive Value HotKnots: 0.624 RNAwolf: 0.520 Number of pairs reference - predicted secondary structure: 875 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs PPfold(seed) Matthews Correlation Coefficient HotKnots: 0.702 PPfold(seed): 0.380 Sensitivity HotKnots: 0.713 PPfold(seed): 0.170 Positive Predictive Value HotKnots: 0.697 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Murlet(seed) Matthews Correlation Coefficient HotKnots: 0.570 Murlet(seed): 0.483 Sensitivity HotKnots: 0.560 Murlet(seed): 0.283 Positive Predictive Value HotKnots: 0.586 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 88 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Alterna Matthews Correlation Coefficient HotKnots: 0.594 Alterna: 0.552 Sensitivity HotKnots: 0.590 Alterna: 0.547 Positive Predictive Value HotKnots: 0.605 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Carnac(seed) Matthews Correlation Coefficient HotKnots: 0.619 Carnac(seed): 0.420 Sensitivity HotKnots: 0.615 Carnac(seed): 0.199 Positive Predictive Value HotKnots: 0.628 Carnac(seed): 0.889 Number of pairs reference - predicted secondary structure: 120 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Vsfold4 Matthews Correlation Coefficient HotKnots: 0.613 Vsfold4: 0.487 Sensitivity HotKnots: 0.607 Vsfold4: 0.446 Positive Predictive Value HotKnots: 0.624 Vsfold4: 0.538 Number of pairs reference - predicted secondary structure: 875 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs RSpredict(seed) Matthews Correlation Coefficient HotKnots: 0.688 RSpredict(seed): 0.381 Sensitivity HotKnots: 0.689 RSpredict(seed): 0.258 Positive Predictive Value HotKnots: 0.691 RSpredict(seed): 0.570 Number of pairs reference - predicted secondary structure: 212 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Vsfold5 Matthews Correlation Coefficient HotKnots: 0.613 Vsfold5: 0.477 Sensitivity HotKnots: 0.607 Vsfold5: 0.451 Positive Predictive Value HotKnots: 0.624 Vsfold5: 0.513 Number of pairs reference - predicted secondary structure: 875 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs RDfolder Matthews Correlation Coefficient HotKnots: 0.594 RDfolder: 0.520 Sensitivity HotKnots: 0.590 RDfolder: 0.464 Positive Predictive Value HotKnots: 0.605 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs MCFold Matthews Correlation Coefficient HotKnots: 0.614 MCFold: 0.473 Sensitivity HotKnots: 0.606 MCFold: 0.524 Positive Predictive Value HotKnots: 0.627 MCFold: 0.434 Number of pairs reference - predicted secondary structure: 760 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs NanoFolder Matthews Correlation Coefficient HotKnots: 0.657 NanoFolder: 0.342 Sensitivity HotKnots: 0.650 NanoFolder: 0.393 Positive Predictive Value HotKnots: 0.668 NanoFolder: 0.307 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ HotKnots vs Mastr(seed) Matthews Correlation Coefficient HotKnots: 0.677 Mastr(seed): 0.267 Sensitivity HotKnots: 0.678 Mastr(seed): 0.091 Positive Predictive Value HotKnots: 0.680 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 230 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNAfold	882 ContextFold vs RNAfold Matthews Correlation Coefficient ContextFold: 0.779 RNAfold: 0.612 Sensitivity ContextFold: 0.741 RNAfold: 0.604 Positive Predictive Value ContextFold: 0.823 RNAfold: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 TurboFold(20) vs RNAfold Matthews Correlation Coefficient TurboFold(20): 0.889 RNAfold: 0.686 Sensitivity TurboFold(20): 0.861 RNAfold: 0.681 Positive Predictive Value TurboFold(20): 0.919 RNAfold: 0.695 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	216 CentroidAlifold(seed) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(seed): 0.790 RNAfold: 0.694 Sensitivity CentroidAlifold(seed): 0.699 RNAfold: 0.691 Positive Predictive Value CentroidAlifold(seed): 0.896 RNAfold: 0.702 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 CentroidHomfold‑LAST vs RNAfold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.736 RNAfold: 0.612 Sensitivity CentroidHomfold‑LAST: 0.665 RNAfold: 0.604 Positive Predictive Value CentroidHomfold‑LAST: 0.818 RNAfold: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	498 PETfold_pre2.0(seed) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.879 RNAfold: 0.659 Sensitivity PETfold_pre2.0(seed): 0.825 RNAfold: 0.659 Positive Predictive Value PETfold_pre2.0(seed): 0.938 RNAfold: 0.663 Number of pairs reference - predicted secondary structure: 498 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 TurboFold(seed) vs RNAfold Matthews Correlation Coefficient TurboFold(seed): 0.798 RNAfold: 0.722 Sensitivity TurboFold(seed): 0.766 RNAfold: 0.714 Positive Predictive Value TurboFold(seed): 0.835 RNAfold: 0.734 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	233 MXScarna(seed) vs RNAfold Matthews Correlation Coefficient MXScarna(seed): 0.750 RNAfold: 0.681 Sensitivity MXScarna(seed): 0.712 RNAfold: 0.678 Positive Predictive Value MXScarna(seed): 0.793 RNAfold: 0.688 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 CentroidAlifold(20) vs RNAfold Matthews Correlation Coefficient CentroidAlifold(20): 0.849 RNAfold: 0.686 Sensitivity CentroidAlifold(20): 0.754 RNAfold: 0.681 Positive Predictive Value CentroidAlifold(20): 0.957 RNAfold: 0.695 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 PETfold_pre2.0(20) vs RNAfold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 RNAfold: 0.686 Sensitivity PETfold_pre2.0(20): 0.737 RNAfold: 0.681 Positive Predictive Value PETfold_pre2.0(20): 0.975 RNAfold: 0.695 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 MXScarna(20) vs RNAfold Matthews Correlation Coefficient MXScarna(20): 0.838 RNAfold: 0.686 Sensitivity MXScarna(20): 0.791 RNAfold: 0.681 Positive Predictive Value MXScarna(20): 0.891 RNAfold: 0.695 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	314 PPfold(20) vs RNAfold Matthews Correlation Coefficient PPfold(20): 0.839 RNAfold: 0.684 Sensitivity PPfold(20): 0.721 RNAfold: 0.679 Positive Predictive Value PPfold(20): 0.977 RNAfold: 0.693 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RNAalifold(20) vs RNAfold Matthews Correlation Coefficient RNAalifold(20): 0.816 RNAfold: 0.686 Sensitivity RNAalifold(20): 0.690 RNAfold: 0.681 Positive Predictive Value RNAalifold(20): 0.966 RNAfold: 0.695 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RSpredict(20) vs RNAfold Matthews Correlation Coefficient RSpredict(20): 0.789 RNAfold: 0.686 Sensitivity RSpredict(20): 0.693 RNAfold: 0.681 Positive Predictive Value RSpredict(20): 0.901 RNAfold: 0.695 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 IPknot vs RNAfold Matthews Correlation Coefficient IPknot: 0.694 RNAfold: 0.612 Sensitivity IPknot: 0.661 RNAfold: 0.604 Positive Predictive Value IPknot: 0.733 RNAfold: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	311 Multilign(20) vs RNAfold Matthews Correlation Coefficient Multilign(20): 0.784 RNAfold: 0.682 Sensitivity Multilign(20): 0.697 RNAfold: 0.678 Positive Predictive Value Multilign(20): 0.885 RNAfold: 0.691 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 CentroidFold vs RNAfold Matthews Correlation Coefficient CentroidFold: 0.645 RNAfold: 0.612 Sensitivity CentroidFold: 0.612 RNAfold: 0.604 Positive Predictive Value CentroidFold: 0.684 RNAfold: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 Contrafold vs RNAfold Matthews Correlation Coefficient Contrafold: 0.643 RNAfold: 0.612 Sensitivity Contrafold: 0.634 RNAfold: 0.604 Positive Predictive Value Contrafold: 0.657 RNAfold: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	315 RNASampler(20) vs RNAfold Matthews Correlation Coefficient RNASampler(20): 0.770 RNAfold: 0.685 Sensitivity RNASampler(20): 0.622 RNAfold: 0.680 Positive Predictive Value RNASampler(20): 0.957 RNAfold: 0.695 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	319 Murlet(20) vs RNAfold Matthews Correlation Coefficient Murlet(20): 0.750 RNAfold: 0.687 Sensitivity Murlet(20): 0.619 RNAfold: 0.682 Positive Predictive Value Murlet(20): 0.913 RNAfold: 0.695 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 CMfinder(seed) vs RNAfold Matthews Correlation Coefficient CMfinder(seed): 0.571 RNAfold: 0.545 Sensitivity CMfinder(seed): 0.439 RNAfold: 0.524 Positive Predictive Value CMfinder(seed): 0.747 RNAfold: 0.572 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 MaxExpect vs RNAfold Matthews Correlation Coefficient MaxExpect: 0.633 RNAfold: 0.612 Sensitivity MaxExpect: 0.617 RNAfold: 0.604 Positive Predictive Value MaxExpect: 0.654 RNAfold: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	316 CMfinder(20) vs RNAfold Matthews Correlation Coefficient CMfinder(20): 0.735 RNAfold: 0.684 Sensitivity CMfinder(20): 0.603 RNAfold: 0.679 Positive Predictive Value CMfinder(20): 0.899 RNAfold: 0.692 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	881 CRWrnafold vs RNAfold Matthews Correlation Coefficient CRWrnafold: 0.630 RNAfold: 0.612 Sensitivity CRWrnafold: 0.618 RNAfold: 0.603 Positive Predictive Value CRWrnafold: 0.648 RNAfold: 0.625 Number of pairs reference - predicted secondary structure: 881 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 ProbKnot vs RNAfold Matthews Correlation Coefficient ProbKnot: 0.630 RNAfold: 0.612 Sensitivity ProbKnot: 0.622 RNAfold: 0.604 Positive Predictive Value ProbKnot: 0.644 RNAfold: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 Mastr(20) vs RNAfold Matthews Correlation Coefficient Mastr(20): 0.708 RNAfold: 0.686 Sensitivity Mastr(20): 0.635 RNAfold: 0.681 Positive Predictive Value Mastr(20): 0.793 RNAfold: 0.695 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 Fold vs RNAfold Matthews Correlation Coefficient Fold: 0.628 RNAfold: 0.612 Sensitivity Fold: 0.620 RNAfold: 0.604 Positive Predictive Value Fold: 0.641 RNAfold: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 UNAFold vs RNAfold Matthews Correlation Coefficient UNAFold: 0.620 RNAfold: 0.612 Sensitivity UNAFold: 0.605 RNAfold: 0.604 Positive Predictive Value UNAFold: 0.639 RNAfold: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 PknotsRG vs RNAfold Matthews Correlation Coefficient PknotsRG: 0.617 RNAfold: 0.612 Sensitivity PknotsRG: 0.610 RNAfold: 0.604 Positive Predictive Value PknotsRG: 0.630 RNAfold: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 Sfold vs RNAfold Matthews Correlation Coefficient Sfold: 0.618 RNAfold: 0.612 Sensitivity Sfold: 0.581 RNAfold: 0.604 Positive Predictive Value Sfold: 0.663 RNAfold: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	205 RNAfold vs RNAalifold(seed) Matthews Correlation Coefficient RNAfold: 0.701 RNAalifold(seed): 0.610 Sensitivity RNAfold: 0.695 RNAalifold(seed): 0.404 Positive Predictive Value RNAfold: 0.710 RNAalifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 RNAsubopt vs RNAfold Matthews Correlation Coefficient RNAsubopt: 0.615 RNAfold: 0.612 Sensitivity RNAsubopt: 0.609 RNAfold: 0.604 Positive Predictive Value RNAsubopt: 0.626 RNAfold: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 4.1569883686e-08	875 HotKnots vs RNAfold Matthews Correlation Coefficient HotKnots: 0.613 RNAfold: 0.612 Sensitivity HotKnots: 0.607 RNAfold: 0.604 Positive Predictive Value HotKnots: 0.624 RNAfold: 0.626 Number of pairs reference - predicted secondary structure: 875 Wilcoxon single-rank test P-value: 0.000230581642477		= RNAshapes vs RNAfold Matthews Correlation Coefficient RNAshapes: 0.612 RNAfold: 0.612 Sensitivity RNAshapes: 0.602 RNAfold: 0.604 Positive Predictive Value RNAshapes: 0.628 RNAfold: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 0.231589081714	+ RNAfold vs RNASampler(seed) Matthews Correlation Coefficient RNAfold: 0.564 RNASampler(seed): 0.557 Sensitivity RNAfold: 0.541 RNASampler(seed): 0.389 Positive Predictive Value RNAfold: 0.591 RNASampler(seed): 0.802 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 1.17668836407e-05	+ RNAfold vs Afold Matthews Correlation Coefficient RNAfold: 0.616 Afold: 0.558 Sensitivity RNAfold: 0.594 Afold: 0.541 Positive Predictive Value RNAfold: 0.644 Afold: 0.582 Number of pairs reference - predicted secondary structure: 530 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Pknots vs RNAfold Matthews Correlation Coefficient Pknots: 0.606 RNAfold: 0.596 Sensitivity Pknots: 0.595 RNAfold: 0.588 Positive Predictive Value Pknots: 0.624 RNAfold: 0.611 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs McQFold Matthews Correlation Coefficient RNAfold: 0.612 McQFold: 0.583 Sensitivity RNAfold: 0.604 McQFold: 0.557 Positive Predictive Value RNAfold: 0.626 McQFold: 0.616 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Carnac(20) Matthews Correlation Coefficient RNAfold: 0.686 Carnac(20): 0.675 Sensitivity RNAfold: 0.681 Carnac(20): 0.500 Positive Predictive Value RNAfold: 0.695 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 9.49173053431e-08	+ RNAfold vs RNASLOpt Matthews Correlation Coefficient RNAfold: 0.612 RNASLOpt: 0.562 Sensitivity RNAfold: 0.604 RNASLOpt: 0.521 Positive Predictive Value RNAfold: 0.626 RNASLOpt: 0.613 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Cylofold Matthews Correlation Coefficient RNAfold: 0.636 Cylofold: 0.577 Sensitivity RNAfold: 0.626 Cylofold: 0.554 Positive Predictive Value RNAfold: 0.653 Cylofold: 0.608 Number of pairs reference - predicted secondary structure: 796 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Multilign(seed) vs RNAfold Matthews Correlation Coefficient Multilign(seed): 0.485 RNAfold: 0.462 Sensitivity Multilign(seed): 0.386 RNAfold: 0.437 Positive Predictive Value Multilign(seed): 0.619 RNAfold: 0.497 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 3.25008686899e-05	+ RNAfold vs RNAwolf Matthews Correlation Coefficient RNAfold: 0.612 RNAwolf: 0.518 Sensitivity RNAfold: 0.604 RNAwolf: 0.523 Positive Predictive Value RNAfold: 0.626 RNAwolf: 0.520 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs PPfold(seed) Matthews Correlation Coefficient RNAfold: 0.701 PPfold(seed): 0.380 Sensitivity RNAfold: 0.702 PPfold(seed): 0.170 Positive Predictive Value RNAfold: 0.705 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Murlet(seed) Matthews Correlation Coefficient RNAfold: 0.596 Murlet(seed): 0.468 Sensitivity RNAfold: 0.576 Murlet(seed): 0.266 Positive Predictive Value RNAfold: 0.622 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Alterna Matthews Correlation Coefficient RNAfold: 0.596 Alterna: 0.552 Sensitivity RNAfold: 0.589 Alterna: 0.547 Positive Predictive Value RNAfold: 0.611 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Carnac(seed) Matthews Correlation Coefficient RNAfold: 0.639 Carnac(seed): 0.415 Sensitivity RNAfold: 0.628 Carnac(seed): 0.196 Positive Predictive Value RNAfold: 0.656 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Vsfold4 Matthews Correlation Coefficient RNAfold: 0.612 Vsfold4: 0.487 Sensitivity RNAfold: 0.604 Vsfold4: 0.447 Positive Predictive Value RNAfold: 0.626 Vsfold4: 0.537 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RSpredict(seed) Matthews Correlation Coefficient RNAfold: 0.694 RSpredict(seed): 0.373 Sensitivity RNAfold: 0.691 RSpredict(seed): 0.251 Positive Predictive Value RNAfold: 0.702 RSpredict(seed): 0.562 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Vsfold5 Matthews Correlation Coefficient RNAfold: 0.612 Vsfold5: 0.477 Sensitivity RNAfold: 0.604 Vsfold5: 0.450 Positive Predictive Value RNAfold: 0.626 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs RDfolder Matthews Correlation Coefficient RNAfold: 0.596 RDfolder: 0.520 Sensitivity RNAfold: 0.589 RDfolder: 0.464 Positive Predictive Value RNAfold: 0.611 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs MCFold Matthews Correlation Coefficient RNAfold: 0.615 MCFold: 0.473 Sensitivity RNAfold: 0.604 MCFold: 0.524 Positive Predictive Value RNAfold: 0.632 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs NanoFolder Matthews Correlation Coefficient RNAfold: 0.643 NanoFolder: 0.335 Sensitivity RNAfold: 0.633 NanoFolder: 0.384 Positive Predictive Value RNAfold: 0.658 NanoFolder: 0.301 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAfold vs Mastr(seed) Matthews Correlation Coefficient RNAfold: 0.681 Mastr(seed): 0.263 Sensitivity RNAfold: 0.678 Mastr(seed): 0.089 Positive Predictive Value RNAfold: 0.688 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNAshapes	882 ContextFold vs RNAshapes Matthews Correlation Coefficient ContextFold: 0.779 RNAshapes: 0.612 Sensitivity ContextFold: 0.741 RNAshapes: 0.602 Positive Predictive Value ContextFold: 0.823 RNAshapes: 0.628 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 TurboFold(20) vs RNAshapes Matthews Correlation Coefficient TurboFold(20): 0.889 RNAshapes: 0.693 Sensitivity TurboFold(20): 0.861 RNAshapes: 0.687 Positive Predictive Value TurboFold(20): 0.919 RNAshapes: 0.702 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	216 CentroidAlifold(seed) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(seed): 0.790 RNAshapes: 0.680 Sensitivity CentroidAlifold(seed): 0.699 RNAshapes: 0.677 Positive Predictive Value CentroidAlifold(seed): 0.896 RNAshapes: 0.686 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 CentroidHomfold‑LAST vs RNAshapes Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.736 RNAshapes: 0.612 Sensitivity CentroidHomfold‑LAST: 0.665 RNAshapes: 0.602 Positive Predictive Value CentroidHomfold‑LAST: 0.818 RNAshapes: 0.628 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	498 PETfold_pre2.0(seed) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.879 RNAshapes: 0.659 Sensitivity PETfold_pre2.0(seed): 0.825 RNAshapes: 0.659 Positive Predictive Value PETfold_pre2.0(seed): 0.938 RNAshapes: 0.664 Number of pairs reference - predicted secondary structure: 498 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 TurboFold(seed) vs RNAshapes Matthews Correlation Coefficient TurboFold(seed): 0.798 RNAshapes: 0.726 Sensitivity TurboFold(seed): 0.766 RNAshapes: 0.717 Positive Predictive Value TurboFold(seed): 0.835 RNAshapes: 0.740 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	233 MXScarna(seed) vs RNAshapes Matthews Correlation Coefficient MXScarna(seed): 0.750 RNAshapes: 0.669 Sensitivity MXScarna(seed): 0.712 RNAshapes: 0.666 Positive Predictive Value MXScarna(seed): 0.793 RNAshapes: 0.676 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 CentroidAlifold(20) vs RNAshapes Matthews Correlation Coefficient CentroidAlifold(20): 0.849 RNAshapes: 0.693 Sensitivity CentroidAlifold(20): 0.754 RNAshapes: 0.687 Positive Predictive Value CentroidAlifold(20): 0.957 RNAshapes: 0.702 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 PETfold_pre2.0(20) vs RNAshapes Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 RNAshapes: 0.693 Sensitivity PETfold_pre2.0(20): 0.737 RNAshapes: 0.687 Positive Predictive Value PETfold_pre2.0(20): 0.975 RNAshapes: 0.702 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 MXScarna(20) vs RNAshapes Matthews Correlation Coefficient MXScarna(20): 0.838 RNAshapes: 0.693 Sensitivity MXScarna(20): 0.791 RNAshapes: 0.687 Positive Predictive Value MXScarna(20): 0.891 RNAshapes: 0.702 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	314 PPfold(20) vs RNAshapes Matthews Correlation Coefficient PPfold(20): 0.839 RNAshapes: 0.692 Sensitivity PPfold(20): 0.721 RNAshapes: 0.686 Positive Predictive Value PPfold(20): 0.977 RNAshapes: 0.701 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RNAalifold(20) vs RNAshapes Matthews Correlation Coefficient RNAalifold(20): 0.816 RNAshapes: 0.693 Sensitivity RNAalifold(20): 0.690 RNAshapes: 0.687 Positive Predictive Value RNAalifold(20): 0.966 RNAshapes: 0.702 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RSpredict(20) vs RNAshapes Matthews Correlation Coefficient RSpredict(20): 0.789 RNAshapes: 0.693 Sensitivity RSpredict(20): 0.693 RNAshapes: 0.687 Positive Predictive Value RSpredict(20): 0.901 RNAshapes: 0.702 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 IPknot vs RNAshapes Matthews Correlation Coefficient IPknot: 0.694 RNAshapes: 0.612 Sensitivity IPknot: 0.661 RNAshapes: 0.602 Positive Predictive Value IPknot: 0.733 RNAshapes: 0.628 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	311 Multilign(20) vs RNAshapes Matthews Correlation Coefficient Multilign(20): 0.784 RNAshapes: 0.689 Sensitivity Multilign(20): 0.697 RNAshapes: 0.683 Positive Predictive Value Multilign(20): 0.885 RNAshapes: 0.699 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 CentroidFold vs RNAshapes Matthews Correlation Coefficient CentroidFold: 0.645 RNAshapes: 0.612 Sensitivity CentroidFold: 0.612 RNAshapes: 0.602 Positive Predictive Value CentroidFold: 0.684 RNAshapes: 0.628 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 Contrafold vs RNAshapes Matthews Correlation Coefficient Contrafold: 0.643 RNAshapes: 0.612 Sensitivity Contrafold: 0.634 RNAshapes: 0.602 Positive Predictive Value Contrafold: 0.657 RNAshapes: 0.628 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	315 RNASampler(20) vs RNAshapes Matthews Correlation Coefficient RNASampler(20): 0.770 RNAshapes: 0.695 Sensitivity RNASampler(20): 0.622 RNAshapes: 0.690 Positive Predictive Value RNASampler(20): 0.957 RNAshapes: 0.705 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	319 Murlet(20) vs RNAshapes Matthews Correlation Coefficient Murlet(20): 0.750 RNAshapes: 0.694 Sensitivity Murlet(20): 0.619 RNAshapes: 0.688 Positive Predictive Value Murlet(20): 0.913 RNAshapes: 0.703 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 CMfinder(seed) vs RNAshapes Matthews Correlation Coefficient CMfinder(seed): 0.571 RNAshapes: 0.539 Sensitivity CMfinder(seed): 0.439 RNAshapes: 0.519 Positive Predictive Value CMfinder(seed): 0.747 RNAshapes: 0.565 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 MaxExpect vs RNAshapes Matthews Correlation Coefficient MaxExpect: 0.633 RNAshapes: 0.612 Sensitivity MaxExpect: 0.617 RNAshapes: 0.602 Positive Predictive Value MaxExpect: 0.654 RNAshapes: 0.628 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	316 CMfinder(20) vs RNAshapes Matthews Correlation Coefficient CMfinder(20): 0.735 RNAshapes: 0.693 Sensitivity CMfinder(20): 0.603 RNAshapes: 0.688 Positive Predictive Value CMfinder(20): 0.899 RNAshapes: 0.702 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	881 CRWrnafold vs RNAshapes Matthews Correlation Coefficient CRWrnafold: 0.630 RNAshapes: 0.612 Sensitivity CRWrnafold: 0.618 RNAshapes: 0.602 Positive Predictive Value CRWrnafold: 0.648 RNAshapes: 0.627 Number of pairs reference - predicted secondary structure: 881 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 ProbKnot vs RNAshapes Matthews Correlation Coefficient ProbKnot: 0.630 RNAshapes: 0.612 Sensitivity ProbKnot: 0.622 RNAshapes: 0.602 Positive Predictive Value ProbKnot: 0.644 RNAshapes: 0.628 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 Mastr(20) vs RNAshapes Matthews Correlation Coefficient Mastr(20): 0.708 RNAshapes: 0.693 Sensitivity Mastr(20): 0.635 RNAshapes: 0.687 Positive Predictive Value Mastr(20): 0.793 RNAshapes: 0.702 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.85233844192e-08	882 Fold vs RNAshapes Matthews Correlation Coefficient Fold: 0.628 RNAshapes: 0.612 Sensitivity Fold: 0.620 RNAshapes: 0.602 Positive Predictive Value Fold: 0.641 RNAshapes: 0.628 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 UNAFold vs RNAshapes Matthews Correlation Coefficient UNAFold: 0.620 RNAshapes: 0.612 Sensitivity UNAFold: 0.605 RNAshapes: 0.602 Positive Predictive Value UNAFold: 0.639 RNAshapes: 0.628 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 PknotsRG vs RNAshapes Matthews Correlation Coefficient PknotsRG: 0.617 RNAshapes: 0.612 Sensitivity PknotsRG: 0.610 RNAshapes: 0.602 Positive Predictive Value PknotsRG: 0.630 RNAshapes: 0.628 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 Sfold vs RNAshapes Matthews Correlation Coefficient Sfold: 0.618 RNAshapes: 0.612 Sensitivity Sfold: 0.581 RNAshapes: 0.602 Positive Predictive Value Sfold: 0.663 RNAshapes: 0.628 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	205 RNAshapes vs RNAalifold(seed) Matthews Correlation Coefficient RNAshapes: 0.686 RNAalifold(seed): 0.610 Sensitivity RNAshapes: 0.681 RNAalifold(seed): 0.404 Positive Predictive Value RNAshapes: 0.695 RNAalifold(seed): 0.923 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 RNAsubopt vs RNAshapes Matthews Correlation Coefficient RNAsubopt: 0.615 RNAshapes: 0.612 Sensitivity RNAsubopt: 0.609 RNAshapes: 0.602 Positive Predictive Value RNAsubopt: 0.626 RNAshapes: 0.628 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 8.1815824276e-08	875 RNAshapes vs HotKnots Matthews Correlation Coefficient RNAshapes: 0.613 HotKnots: 0.613 Sensitivity RNAshapes: 0.603 HotKnots: 0.607 Positive Predictive Value RNAshapes: 0.628 HotKnots: 0.624 Number of pairs reference - predicted secondary structure: 875 Wilcoxon single-rank test P-value: 0.0738256256282	882 RNAshapes vs RNAfold Matthews Correlation Coefficient RNAshapes: 0.612 RNAfold: 0.612 Sensitivity RNAshapes: 0.602 RNAfold: 0.604 Positive Predictive Value RNAshapes: 0.628 RNAfold: 0.626 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 0.231589081714		= RNAshapes vs RNASampler(seed) Matthews Correlation Coefficient RNAshapes: 0.557 RNASampler(seed): 0.557 Sensitivity RNAshapes: 0.536 RNASampler(seed): 0.389 Positive Predictive Value RNAshapes: 0.585 RNASampler(seed): 0.802 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 0.300678301565	+ RNAshapes vs Afold Matthews Correlation Coefficient RNAshapes: 0.621 Afold: 0.558 Sensitivity RNAshapes: 0.597 Afold: 0.541 Positive Predictive Value RNAshapes: 0.651 Afold: 0.582 Number of pairs reference - predicted secondary structure: 530 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Pknots vs RNAshapes Matthews Correlation Coefficient Pknots: 0.606 RNAshapes: 0.594 Sensitivity Pknots: 0.595 RNAshapes: 0.585 Positive Predictive Value Pknots: 0.624 RNAshapes: 0.610 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs McQFold Matthews Correlation Coefficient RNAshapes: 0.612 McQFold: 0.583 Sensitivity RNAshapes: 0.602 McQFold: 0.557 Positive Predictive Value RNAshapes: 0.628 McQFold: 0.616 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Carnac(20) Matthews Correlation Coefficient RNAshapes: 0.693 Carnac(20): 0.675 Sensitivity RNAshapes: 0.687 Carnac(20): 0.500 Positive Predictive Value RNAshapes: 0.702 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs RNASLOpt Matthews Correlation Coefficient RNAshapes: 0.612 RNASLOpt: 0.562 Sensitivity RNAshapes: 0.602 RNASLOpt: 0.521 Positive Predictive Value RNAshapes: 0.628 RNASLOpt: 0.613 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Cylofold Matthews Correlation Coefficient RNAshapes: 0.634 Cylofold: 0.577 Sensitivity RNAshapes: 0.623 Cylofold: 0.554 Positive Predictive Value RNAshapes: 0.651 Cylofold: 0.608 Number of pairs reference - predicted secondary structure: 796 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Multilign(seed) vs RNAshapes Matthews Correlation Coefficient Multilign(seed): 0.485 RNAshapes: 0.468 Sensitivity Multilign(seed): 0.386 RNAshapes: 0.437 Positive Predictive Value Multilign(seed): 0.619 RNAshapes: 0.511 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.66432434427e-06	+ RNAshapes vs RNAwolf Matthews Correlation Coefficient RNAshapes: 0.612 RNAwolf: 0.518 Sensitivity RNAshapes: 0.602 RNAwolf: 0.523 Positive Predictive Value RNAshapes: 0.628 RNAwolf: 0.520 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs PPfold(seed) Matthews Correlation Coefficient RNAshapes: 0.705 PPfold(seed): 0.380 Sensitivity RNAshapes: 0.705 PPfold(seed): 0.170 Positive Predictive Value RNAshapes: 0.709 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Murlet(seed) Matthews Correlation Coefficient RNAshapes: 0.592 Murlet(seed): 0.468 Sensitivity RNAshapes: 0.572 Murlet(seed): 0.266 Positive Predictive Value RNAshapes: 0.617 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Alterna Matthews Correlation Coefficient RNAshapes: 0.596 Alterna: 0.552 Sensitivity RNAshapes: 0.587 Alterna: 0.547 Positive Predictive Value RNAshapes: 0.612 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Carnac(seed) Matthews Correlation Coefficient RNAshapes: 0.632 Carnac(seed): 0.415 Sensitivity RNAshapes: 0.621 Carnac(seed): 0.196 Positive Predictive Value RNAshapes: 0.649 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Vsfold4 Matthews Correlation Coefficient RNAshapes: 0.612 Vsfold4: 0.487 Sensitivity RNAshapes: 0.602 Vsfold4: 0.447 Positive Predictive Value RNAshapes: 0.628 Vsfold4: 0.537 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs RSpredict(seed) Matthews Correlation Coefficient RNAshapes: 0.680 RSpredict(seed): 0.373 Sensitivity RNAshapes: 0.677 RSpredict(seed): 0.251 Positive Predictive Value RNAshapes: 0.686 RSpredict(seed): 0.562 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Vsfold5 Matthews Correlation Coefficient RNAshapes: 0.612 Vsfold5: 0.477 Sensitivity RNAshapes: 0.602 Vsfold5: 0.450 Positive Predictive Value RNAshapes: 0.628 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs RDfolder Matthews Correlation Coefficient RNAshapes: 0.596 RDfolder: 0.520 Sensitivity RNAshapes: 0.587 RDfolder: 0.464 Positive Predictive Value RNAshapes: 0.612 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs MCFold Matthews Correlation Coefficient RNAshapes: 0.617 MCFold: 0.473 Sensitivity RNAshapes: 0.605 MCFold: 0.524 Positive Predictive Value RNAshapes: 0.635 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs NanoFolder Matthews Correlation Coefficient RNAshapes: 0.648 NanoFolder: 0.335 Sensitivity RNAshapes: 0.635 NanoFolder: 0.384 Positive Predictive Value RNAshapes: 0.665 NanoFolder: 0.301 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAshapes vs Mastr(seed) Matthews Correlation Coefficient RNAshapes: 0.669 Mastr(seed): 0.263 Sensitivity RNAshapes: 0.666 Mastr(seed): 0.089 Positive Predictive Value RNAshapes: 0.676 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNASampler(seed)	86 ContextFold vs RNASampler(seed) Matthews Correlation Coefficient ContextFold: 0.692 RNASampler(seed): 0.557 Sensitivity ContextFold: 0.637 RNASampler(seed): 0.389 Positive Predictive Value ContextFold: 0.755 RNASampler(seed): 0.802 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	42 TurboFold(20) vs RNASampler(seed) Matthews Correlation Coefficient TurboFold(20): 0.769 RNASampler(seed): 0.571 Sensitivity TurboFold(20): 0.707 RNASampler(seed): 0.343 Positive Predictive Value TurboFold(20): 0.841 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	86 CentroidAlifold(seed) vs RNASampler(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.810 RNASampler(seed): 0.557 Sensitivity CentroidAlifold(seed): 0.674 RNASampler(seed): 0.389 Positive Predictive Value CentroidAlifold(seed): 0.976 RNASampler(seed): 0.802 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	86 CentroidHomfold‑LAST vs RNASampler(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.714 RNASampler(seed): 0.557 Sensitivity CentroidHomfold‑LAST: 0.637 RNASampler(seed): 0.389 Positive Predictive Value CentroidHomfold‑LAST: 0.805 RNASampler(seed): 0.802 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	86 PETfold_pre2.0(seed) vs RNASampler(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.749 RNASampler(seed): 0.557 Sensitivity PETfold_pre2.0(seed): 0.650 RNASampler(seed): 0.389 Positive Predictive Value PETfold_pre2.0(seed): 0.866 RNASampler(seed): 0.802 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	22 TurboFold(seed) vs RNASampler(seed) Matthews Correlation Coefficient TurboFold(seed): 0.697 RNASampler(seed): 0.561 Sensitivity TurboFold(seed): 0.626 RNASampler(seed): 0.414 Positive Predictive Value TurboFold(seed): 0.780 RNASampler(seed): 0.765 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 4.94031556815e-08	86 MXScarna(seed) vs RNASampler(seed) Matthews Correlation Coefficient MXScarna(seed): 0.706 RNASampler(seed): 0.557 Sensitivity MXScarna(seed): 0.670 RNASampler(seed): 0.389 Positive Predictive Value MXScarna(seed): 0.748 RNASampler(seed): 0.802 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	42 CentroidAlifold(20) vs RNASampler(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.822 RNASampler(seed): 0.571 Sensitivity CentroidAlifold(20): 0.739 RNASampler(seed): 0.343 Positive Predictive Value CentroidAlifold(20): 0.917 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	42 PETfold_pre2.0(20) vs RNASampler(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.735 RNASampler(seed): 0.571 Sensitivity PETfold_pre2.0(20): 0.627 RNASampler(seed): 0.343 Positive Predictive Value PETfold_pre2.0(20): 0.867 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	42 MXScarna(20) vs RNASampler(seed) Matthews Correlation Coefficient MXScarna(20): 0.835 RNASampler(seed): 0.571 Sensitivity MXScarna(20): 0.800 RNASampler(seed): 0.343 Positive Predictive Value MXScarna(20): 0.874 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	42 PPfold(20) vs RNASampler(seed) Matthews Correlation Coefficient PPfold(20): 0.690 RNASampler(seed): 0.571 Sensitivity PPfold(20): 0.547 RNASampler(seed): 0.343 Positive Predictive Value PPfold(20): 0.876 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	42 RNAalifold(20) vs RNASampler(seed) Matthews Correlation Coefficient RNAalifold(20): 0.659 RNASampler(seed): 0.571 Sensitivity RNAalifold(20): 0.511 RNASampler(seed): 0.343 Positive Predictive Value RNAalifold(20): 0.857 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	42 RSpredict(20) vs RNASampler(seed) Matthews Correlation Coefficient RSpredict(20): 0.753 RNASampler(seed): 0.571 Sensitivity RSpredict(20): 0.684 RNASampler(seed): 0.343 Positive Predictive Value RSpredict(20): 0.833 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 5.23657817852e-08	86 IPknot vs RNASampler(seed) Matthews Correlation Coefficient IPknot: 0.635 RNASampler(seed): 0.557 Sensitivity IPknot: 0.572 RNASampler(seed): 0.389 Positive Predictive Value IPknot: 0.709 RNASampler(seed): 0.802 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	42 Multilign(20) vs RNASampler(seed) Matthews Correlation Coefficient Multilign(20): 0.692 RNASampler(seed): 0.571 Sensitivity Multilign(20): 0.552 RNASampler(seed): 0.343 Positive Predictive Value Multilign(20): 0.874 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	86 CentroidFold vs RNASampler(seed) Matthews Correlation Coefficient CentroidFold: 0.614 RNASampler(seed): 0.557 Sensitivity CentroidFold: 0.530 RNASampler(seed): 0.389 Positive Predictive Value CentroidFold: 0.714 RNASampler(seed): 0.802 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	86 Contrafold vs RNASampler(seed) Matthews Correlation Coefficient Contrafold: 0.609 RNASampler(seed): 0.557 Sensitivity Contrafold: 0.561 RNASampler(seed): 0.389 Positive Predictive Value Contrafold: 0.665 RNASampler(seed): 0.802 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	42 RNASampler(20) vs RNASampler(seed) Matthews Correlation Coefficient RNASampler(20): 0.640 RNASampler(seed): 0.571 Sensitivity RNASampler(20): 0.454 RNASampler(seed): 0.343 Positive Predictive Value RNASampler(20): 0.909 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 5.23657817852e-08	42 Murlet(20) vs RNASampler(seed) Matthews Correlation Coefficient Murlet(20): 0.685 RNASampler(seed): 0.571 Sensitivity Murlet(20): 0.527 RNASampler(seed): 0.343 Positive Predictive Value Murlet(20): 0.896 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 CMfinder(seed) vs RNASampler(seed) Matthews Correlation Coefficient CMfinder(seed): 0.571 RNASampler(seed): 0.554 Sensitivity CMfinder(seed): 0.439 RNASampler(seed): 0.388 Positive Predictive Value CMfinder(seed): 0.747 RNASampler(seed): 0.795 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 7.04732813174e-08	86 MaxExpect vs RNASampler(seed) Matthews Correlation Coefficient MaxExpect: 0.604 RNASampler(seed): 0.557 Sensitivity MaxExpect: 0.567 RNASampler(seed): 0.389 Positive Predictive Value MaxExpect: 0.648 RNASampler(seed): 0.802 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	42 CMfinder(20) vs RNASampler(seed) Matthews Correlation Coefficient CMfinder(20): 0.735 RNASampler(seed): 0.571 Sensitivity CMfinder(20): 0.607 RNASampler(seed): 0.343 Positive Predictive Value CMfinder(20): 0.894 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	86 RNASampler(seed) vs CRWrnafold Matthews Correlation Coefficient RNASampler(seed): 0.557 CRWrnafold: 0.473 Sensitivity RNASampler(seed): 0.389 CRWrnafold: 0.451 Positive Predictive Value RNASampler(seed): 0.802 CRWrnafold: 0.501 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	86 ProbKnot vs RNASampler(seed) Matthews Correlation Coefficient ProbKnot: 0.582 RNASampler(seed): 0.557 Sensitivity ProbKnot: 0.554 RNASampler(seed): 0.389 Positive Predictive Value ProbKnot: 0.615 RNASampler(seed): 0.802 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	42 Mastr(20) vs RNASampler(seed) Matthews Correlation Coefficient Mastr(20): 0.773 RNASampler(seed): 0.571 Sensitivity Mastr(20): 0.712 RNASampler(seed): 0.343 Positive Predictive Value Mastr(20): 0.843 RNASampler(seed): 0.957 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	86 Fold vs RNASampler(seed) Matthews Correlation Coefficient Fold: 0.587 RNASampler(seed): 0.557 Sensitivity Fold: 0.564 RNASampler(seed): 0.389 Positive Predictive Value Fold: 0.616 RNASampler(seed): 0.802 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	86 UNAFold vs RNASampler(seed) Matthews Correlation Coefficient UNAFold: 0.597 RNASampler(seed): 0.557 Sensitivity UNAFold: 0.570 RNASampler(seed): 0.389 Positive Predictive Value UNAFold: 0.629 RNASampler(seed): 0.802 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	86 PknotsRG vs RNASampler(seed) Matthews Correlation Coefficient PknotsRG: 0.622 RNASampler(seed): 0.557 Sensitivity PknotsRG: 0.606 RNASampler(seed): 0.389 Positive Predictive Value PknotsRG: 0.643 RNASampler(seed): 0.802 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	86 Sfold vs RNASampler(seed) Matthews Correlation Coefficient Sfold: 0.565 RNASampler(seed): 0.557 Sensitivity Sfold: 0.516 RNASampler(seed): 0.389 Positive Predictive Value Sfold: 0.625 RNASampler(seed): 0.802 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 9.69999390915e-05	86 RNAalifold(seed) vs RNASampler(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.657 RNASampler(seed): 0.557 Sensitivity RNAalifold(seed): 0.501 RNASampler(seed): 0.389 Positive Predictive Value RNAalifold(seed): 0.865 RNASampler(seed): 0.802 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	86 RNASampler(seed) vs RNAsubopt Matthews Correlation Coefficient RNASampler(seed): 0.557 RNAsubopt: 0.547 Sensitivity RNASampler(seed): 0.389 RNAsubopt: 0.529 Positive Predictive Value RNASampler(seed): 0.802 RNAsubopt: 0.570 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 6.58294707158e-07	83 RNASampler(seed) vs HotKnots Matthews Correlation Coefficient RNASampler(seed): 0.538 HotKnots: 0.533 Sensitivity RNASampler(seed): 0.371 HotKnots: 0.522 Positive Predictive Value RNASampler(seed): 0.786 HotKnots: 0.550 Number of pairs reference - predicted secondary structure: 83 Wilcoxon single-rank test P-value: 0.00842627253913	86 RNAfold vs RNASampler(seed) Matthews Correlation Coefficient RNAfold: 0.564 RNASampler(seed): 0.557 Sensitivity RNAfold: 0.541 RNASampler(seed): 0.389 Positive Predictive Value RNAfold: 0.591 RNASampler(seed): 0.802 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 1.17668836407e-05	86 RNAshapes vs RNASampler(seed) Matthews Correlation Coefficient RNAshapes: 0.557 RNASampler(seed): 0.557 Sensitivity RNAshapes: 0.536 RNASampler(seed): 0.389 Positive Predictive Value RNAshapes: 0.585 RNASampler(seed): 0.802 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 0.300678301565		- Afold vs RNASampler(seed) Matthews Correlation Coefficient Afold: 0.590 RNASampler(seed): 0.566 Sensitivity Afold: 0.573 RNASampler(seed): 0.394 Positive Predictive Value Afold: 0.612 RNASampler(seed): 0.817 Number of pairs reference - predicted secondary structure: 79 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(seed) vs Pknots Matthews Correlation Coefficient RNASampler(seed): 0.455 Pknots: 0.446 Sensitivity RNASampler(seed): 0.284 Pknots: 0.429 Positive Predictive Value RNASampler(seed): 0.738 Pknots: 0.475 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 5.21379515797e-05	= McQFold vs RNASampler(seed) Matthews Correlation Coefficient McQFold: 0.560 RNASampler(seed): 0.557 Sensitivity McQFold: 0.514 RNASampler(seed): 0.389 Positive Predictive Value McQFold: 0.614 RNASampler(seed): 0.802 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 0.192299791283	+ RNASampler(seed) vs Carnac(20) Matthews Correlation Coefficient RNASampler(seed): 0.571 Carnac(20): 0.461 Sensitivity RNASampler(seed): 0.343 Carnac(20): 0.241 Positive Predictive Value RNASampler(seed): 0.957 Carnac(20): 0.893 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(seed) vs RNASLOpt Matthews Correlation Coefficient RNASampler(seed): 0.557 RNASLOpt: 0.515 Sensitivity RNASampler(seed): 0.389 RNASLOpt: 0.451 Positive Predictive Value RNASampler(seed): 0.802 RNASLOpt: 0.594 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(seed) vs Cylofold Matthews Correlation Coefficient RNASampler(seed): 0.514 Cylofold: 0.503 Sensitivity RNASampler(seed): 0.335 Cylofold: 0.455 Positive Predictive Value RNASampler(seed): 0.797 Cylofold: 0.565 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 1.80472700427e-05	+ RNASampler(seed) vs Multilign(seed) Matthews Correlation Coefficient RNASampler(seed): 0.497 Multilign(seed): 0.485 Sensitivity RNASampler(seed): 0.381 Multilign(seed): 0.386 Positive Predictive Value RNASampler(seed): 0.656 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 5.14700275415e-08	+ RNASampler(seed) vs RNAwolf Matthews Correlation Coefficient RNASampler(seed): 0.557 RNAwolf: 0.383 Sensitivity RNASampler(seed): 0.389 RNAwolf: 0.383 Positive Predictive Value RNASampler(seed): 0.802 RNAwolf: 0.391 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	- PPfold(seed) vs RNASampler(seed) Matthews Correlation Coefficient PPfold(seed): 0.686 RNASampler(seed): 0.486 Sensitivity PPfold(seed): 0.555 RNASampler(seed): 0.345 Positive Predictive Value PPfold(seed): 0.852 RNASampler(seed): 0.693 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.66715895098e-08	+ RNASampler(seed) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(seed): 0.557 Murlet(seed): 0.473 Sensitivity RNASampler(seed): 0.389 Murlet(seed): 0.276 Positive Predictive Value RNASampler(seed): 0.802 Murlet(seed): 0.818 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(seed) vs Alterna Matthews Correlation Coefficient RNASampler(seed): 0.455 Alterna: 0.449 Sensitivity RNASampler(seed): 0.284 Alterna: 0.422 Positive Predictive Value RNASampler(seed): 0.738 Alterna: 0.490 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 0.000167509336666	+ RNASampler(seed) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(seed): 0.557 Carnac(seed): 0.450 Sensitivity RNASampler(seed): 0.389 Carnac(seed): 0.239 Positive Predictive Value RNASampler(seed): 0.802 Carnac(seed): 0.852 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(seed) vs Vsfold4 Matthews Correlation Coefficient RNASampler(seed): 0.557 Vsfold4: 0.411 Sensitivity RNASampler(seed): 0.389 Vsfold4: 0.363 Positive Predictive Value RNASampler(seed): 0.802 Vsfold4: 0.472 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(seed): 0.557 RSpredict(seed): 0.511 Sensitivity RNASampler(seed): 0.389 RSpredict(seed): 0.405 Positive Predictive Value RNASampler(seed): 0.802 RSpredict(seed): 0.651 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(seed) vs Vsfold5 Matthews Correlation Coefficient RNASampler(seed): 0.557 Vsfold5: 0.390 Sensitivity RNASampler(seed): 0.389 Vsfold5: 0.356 Positive Predictive Value RNASampler(seed): 0.802 Vsfold5: 0.434 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(seed) vs RDfolder Matthews Correlation Coefficient RNASampler(seed): 0.455 RDfolder: 0.357 Sensitivity RNASampler(seed): 0.284 RDfolder: 0.288 Positive Predictive Value RNASampler(seed): 0.738 RDfolder: 0.456 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(seed) vs MCFold Matthews Correlation Coefficient RNASampler(seed): 0.502 MCFold: 0.422 Sensitivity RNASampler(seed): 0.334 MCFold: 0.464 Positive Predictive Value RNASampler(seed): 0.760 MCFold: 0.391 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASampler(seed) vs NanoFolder Matthews Correlation Coefficient RNASampler(seed): 0.461 NanoFolder: 0.413 Sensitivity RNASampler(seed): 0.281 NanoFolder: 0.464 Positive Predictive Value RNASampler(seed): 0.763 NanoFolder: 0.375 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 4.30260184036e-08	+ RNASampler(seed) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(seed): 0.557 Mastr(seed): 0.490 Sensitivity RNASampler(seed): 0.389 Mastr(seed): 0.307 Positive Predictive Value RNASampler(seed): 0.802 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08
Afold	530 ContextFold vs Afold Matthews Correlation Coefficient ContextFold: 0.718 Afold: 0.558 Sensitivity ContextFold: 0.673 Afold: 0.541 Positive Predictive Value ContextFold: 0.770 Afold: 0.582 Number of pairs reference - predicted secondary structure: 530 Wilcoxon single-rank test P-value: 3.56938820447e-08	163 TurboFold(20) vs Afold Matthews Correlation Coefficient TurboFold(20): 0.858 Afold: 0.643 Sensitivity TurboFold(20): 0.826 Afold: 0.632 Positive Predictive Value TurboFold(20): 0.893 Afold: 0.659 Number of pairs reference - predicted secondary structure: 163 Wilcoxon single-rank test P-value: 3.56938820447e-08	162 CentroidAlifold(seed) vs Afold Matthews Correlation Coefficient CentroidAlifold(seed): 0.811 Afold: 0.649 Sensitivity CentroidAlifold(seed): 0.727 Afold: 0.646 Positive Predictive Value CentroidAlifold(seed): 0.906 Afold: 0.657 Number of pairs reference - predicted secondary structure: 162 Wilcoxon single-rank test P-value: 3.56938820447e-08	530 CentroidHomfold‑LAST vs Afold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.676 Afold: 0.558 Sensitivity CentroidHomfold‑LAST: 0.596 Afold: 0.541 Positive Predictive Value CentroidHomfold‑LAST: 0.771 Afold: 0.582 Number of pairs reference - predicted secondary structure: 530 Wilcoxon single-rank test P-value: 3.56938820447e-08	233 PETfold_pre2.0(seed) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.825 Afold: 0.627 Sensitivity PETfold_pre2.0(seed): 0.751 Afold: 0.616 Positive Predictive Value PETfold_pre2.0(seed): 0.908 Afold: 0.642 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	28 TurboFold(seed) vs Afold Matthews Correlation Coefficient TurboFold(seed): 0.797 Afold: 0.671 Sensitivity TurboFold(seed): 0.758 Afold: 0.657 Positive Predictive Value TurboFold(seed): 0.841 Afold: 0.689 Number of pairs reference - predicted secondary structure: 28 Wilcoxon single-rank test P-value: 5.10776592382e-08	167 MXScarna(seed) vs Afold Matthews Correlation Coefficient MXScarna(seed): 0.744 Afold: 0.641 Sensitivity MXScarna(seed): 0.707 Afold: 0.637 Positive Predictive Value MXScarna(seed): 0.786 Afold: 0.649 Number of pairs reference - predicted secondary structure: 167 Wilcoxon single-rank test P-value: 3.56938820447e-08	163 CentroidAlifold(20) vs Afold Matthews Correlation Coefficient CentroidAlifold(20): 0.792 Afold: 0.643 Sensitivity CentroidAlifold(20): 0.668 Afold: 0.632 Positive Predictive Value CentroidAlifold(20): 0.941 Afold: 0.659 Number of pairs reference - predicted secondary structure: 163 Wilcoxon single-rank test P-value: 3.56938820447e-08	163 PETfold_pre2.0(20) vs Afold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.777 Afold: 0.643 Sensitivity PETfold_pre2.0(20): 0.632 Afold: 0.632 Positive Predictive Value PETfold_pre2.0(20): 0.957 Afold: 0.659 Number of pairs reference - predicted secondary structure: 163 Wilcoxon single-rank test P-value: 3.56938820447e-08	163 MXScarna(20) vs Afold Matthews Correlation Coefficient MXScarna(20): 0.805 Afold: 0.643 Sensitivity MXScarna(20): 0.751 Afold: 0.632 Positive Predictive Value MXScarna(20): 0.865 Afold: 0.659 Number of pairs reference - predicted secondary structure: 163 Wilcoxon single-rank test P-value: 3.56938820447e-08	159 PPfold(20) vs Afold Matthews Correlation Coefficient PPfold(20): 0.764 Afold: 0.640 Sensitivity PPfold(20): 0.610 Afold: 0.628 Positive Predictive Value PPfold(20): 0.960 Afold: 0.657 Number of pairs reference - predicted secondary structure: 159 Wilcoxon single-rank test P-value: 3.56938820447e-08	163 RNAalifold(20) vs Afold Matthews Correlation Coefficient RNAalifold(20): 0.741 Afold: 0.643 Sensitivity RNAalifold(20): 0.580 Afold: 0.632 Positive Predictive Value RNAalifold(20): 0.950 Afold: 0.659 Number of pairs reference - predicted secondary structure: 163 Wilcoxon single-rank test P-value: 3.56938820447e-08	163 RSpredict(20) vs Afold Matthews Correlation Coefficient RSpredict(20): 0.775 Afold: 0.643 Sensitivity RSpredict(20): 0.677 Afold: 0.632 Positive Predictive Value RSpredict(20): 0.890 Afold: 0.659 Number of pairs reference - predicted secondary structure: 163 Wilcoxon single-rank test P-value: 3.56938820447e-08	530 IPknot vs Afold Matthews Correlation Coefficient IPknot: 0.669 Afold: 0.558 Sensitivity IPknot: 0.626 Afold: 0.541 Positive Predictive Value IPknot: 0.719 Afold: 0.582 Number of pairs reference - predicted secondary structure: 530 Wilcoxon single-rank test P-value: 3.56938820447e-08	155 Multilign(20) vs Afold Matthews Correlation Coefficient Multilign(20): 0.728 Afold: 0.643 Sensitivity Multilign(20): 0.617 Afold: 0.631 Positive Predictive Value Multilign(20): 0.863 Afold: 0.659 Number of pairs reference - predicted secondary structure: 155 Wilcoxon single-rank test P-value: 3.56938820447e-08	530 CentroidFold vs Afold Matthews Correlation Coefficient CentroidFold: 0.609 Afold: 0.558 Sensitivity CentroidFold: 0.570 Afold: 0.541 Positive Predictive Value CentroidFold: 0.655 Afold: 0.582 Number of pairs reference - predicted secondary structure: 530 Wilcoxon single-rank test P-value: 3.56938820447e-08	530 Contrafold vs Afold Matthews Correlation Coefficient Contrafold: 0.609 Afold: 0.558 Sensitivity Contrafold: 0.592 Afold: 0.541 Positive Predictive Value Contrafold: 0.631 Afold: 0.582 Number of pairs reference - predicted secondary structure: 530 Wilcoxon single-rank test P-value: 3.56938820447e-08	158 RNASampler(20) vs Afold Matthews Correlation Coefficient RNASampler(20): 0.683 Afold: 0.649 Sensitivity RNASampler(20): 0.500 Afold: 0.636 Positive Predictive Value RNASampler(20): 0.937 Afold: 0.667 Number of pairs reference - predicted secondary structure: 158 Wilcoxon single-rank test P-value: 3.56938820447e-08	163 Murlet(20) vs Afold Matthews Correlation Coefficient Murlet(20): 0.714 Afold: 0.643 Sensitivity Murlet(20): 0.547 Afold: 0.632 Positive Predictive Value Murlet(20): 0.935 Afold: 0.659 Number of pairs reference - predicted secondary structure: 163 Wilcoxon single-rank test P-value: 3.56938820447e-08	71 CMfinder(seed) vs Afold Matthews Correlation Coefficient CMfinder(seed): 0.590 Afold: 0.573 Sensitivity CMfinder(seed): 0.463 Afold: 0.557 Positive Predictive Value CMfinder(seed): 0.758 Afold: 0.594 Number of pairs reference - predicted secondary structure: 71 Wilcoxon single-rank test P-value: 8.1815824276e-08	530 MaxExpect vs Afold Matthews Correlation Coefficient MaxExpect: 0.622 Afold: 0.558 Sensitivity MaxExpect: 0.596 Afold: 0.541 Positive Predictive Value MaxExpect: 0.654 Afold: 0.582 Number of pairs reference - predicted secondary structure: 530 Wilcoxon single-rank test P-value: 3.56938820447e-08	161 CMfinder(20) vs Afold Matthews Correlation Coefficient CMfinder(20): 0.691 Afold: 0.642 Sensitivity CMfinder(20): 0.557 Afold: 0.630 Positive Predictive Value CMfinder(20): 0.861 Afold: 0.658 Number of pairs reference - predicted secondary structure: 161 Wilcoxon single-rank test P-value: 3.56938820447e-08	529 CRWrnafold vs Afold Matthews Correlation Coefficient CRWrnafold: 0.607 Afold: 0.558 Sensitivity CRWrnafold: 0.583 Afold: 0.541 Positive Predictive Value CRWrnafold: 0.637 Afold: 0.581 Number of pairs reference - predicted secondary structure: 529 Wilcoxon single-rank test P-value: 3.56938820447e-08	530 ProbKnot vs Afold Matthews Correlation Coefficient ProbKnot: 0.616 Afold: 0.558 Sensitivity ProbKnot: 0.594 Afold: 0.541 Positive Predictive Value ProbKnot: 0.645 Afold: 0.582 Number of pairs reference - predicted secondary structure: 530 Wilcoxon single-rank test P-value: 3.56938820447e-08	163 Mastr(20) vs Afold Matthews Correlation Coefficient Mastr(20): 0.688 Afold: 0.643 Sensitivity Mastr(20): 0.602 Afold: 0.632 Positive Predictive Value Mastr(20): 0.789 Afold: 0.659 Number of pairs reference - predicted secondary structure: 163 Wilcoxon single-rank test P-value: 3.56938820447e-08	530 Fold vs Afold Matthews Correlation Coefficient Fold: 0.617 Afold: 0.558 Sensitivity Fold: 0.599 Afold: 0.541 Positive Predictive Value Fold: 0.642 Afold: 0.582 Number of pairs reference - predicted secondary structure: 530 Wilcoxon single-rank test P-value: 3.56938820447e-08	530 UNAFold vs Afold Matthews Correlation Coefficient UNAFold: 0.624 Afold: 0.558 Sensitivity UNAFold: 0.597 Afold: 0.541 Positive Predictive Value UNAFold: 0.658 Afold: 0.582 Number of pairs reference - predicted secondary structure: 530 Wilcoxon single-rank test P-value: 3.56938820447e-08	530 PknotsRG vs Afold Matthews Correlation Coefficient PknotsRG: 0.622 Afold: 0.558 Sensitivity PknotsRG: 0.602 Afold: 0.541 Positive Predictive Value PknotsRG: 0.649 Afold: 0.582 Number of pairs reference - predicted secondary structure: 530 Wilcoxon single-rank test P-value: 3.56938820447e-08	530 Sfold vs Afold Matthews Correlation Coefficient Sfold: 0.619 Afold: 0.558 Sensitivity Sfold: 0.574 Afold: 0.541 Positive Predictive Value Sfold: 0.673 Afold: 0.582 Number of pairs reference - predicted secondary structure: 530 Wilcoxon single-rank test P-value: 3.56938820447e-08	162 Afold vs RNAalifold(seed) Matthews Correlation Coefficient Afold: 0.649 RNAalifold(seed): 0.626 Sensitivity Afold: 0.646 RNAalifold(seed): 0.424 Positive Predictive Value Afold: 0.657 RNAalifold(seed): 0.927 Number of pairs reference - predicted secondary structure: 162 Wilcoxon single-rank test P-value: 3.56938820447e-08	530 RNAsubopt vs Afold Matthews Correlation Coefficient RNAsubopt: 0.604 Afold: 0.558 Sensitivity RNAsubopt: 0.586 Afold: 0.541 Positive Predictive Value RNAsubopt: 0.629 Afold: 0.582 Number of pairs reference - predicted secondary structure: 530 Wilcoxon single-rank test P-value: 3.56938820447e-08	526 HotKnots vs Afold Matthews Correlation Coefficient HotKnots: 0.623 Afold: 0.559 Sensitivity HotKnots: 0.603 Afold: 0.541 Positive Predictive Value HotKnots: 0.650 Afold: 0.583 Number of pairs reference - predicted secondary structure: 526 Wilcoxon single-rank test P-value: 3.56938820447e-08	530 RNAfold vs Afold Matthews Correlation Coefficient RNAfold: 0.616 Afold: 0.558 Sensitivity RNAfold: 0.594 Afold: 0.541 Positive Predictive Value RNAfold: 0.644 Afold: 0.582 Number of pairs reference - predicted secondary structure: 530 Wilcoxon single-rank test P-value: 3.56938820447e-08	530 RNAshapes vs Afold Matthews Correlation Coefficient RNAshapes: 0.621 Afold: 0.558 Sensitivity RNAshapes: 0.597 Afold: 0.541 Positive Predictive Value RNAshapes: 0.651 Afold: 0.582 Number of pairs reference - predicted secondary structure: 530 Wilcoxon single-rank test P-value: 3.56938820447e-08	79 Afold vs RNASampler(seed) Matthews Correlation Coefficient Afold: 0.590 RNASampler(seed): 0.566 Sensitivity Afold: 0.573 RNASampler(seed): 0.394 Positive Predictive Value Afold: 0.612 RNASampler(seed): 0.817 Number of pairs reference - predicted secondary structure: 79 Wilcoxon single-rank test P-value: 3.56938820447e-08		= Afold vs Pknots Matthews Correlation Coefficient Afold: 0.540 Pknots: 0.537 Sensitivity Afold: 0.519 Pknots: 0.511 Positive Predictive Value Afold: 0.572 Pknots: 0.575 Number of pairs reference - predicted secondary structure: 404 Wilcoxon single-rank test P-value: 0.247700967591	+ Afold vs McQFold Matthews Correlation Coefficient Afold: 0.558 McQFold: 0.534 Sensitivity Afold: 0.541 McQFold: 0.501 Positive Predictive Value Afold: 0.582 McQFold: 0.576 Number of pairs reference - predicted secondary structure: 530 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs Carnac(20) Matthews Correlation Coefficient Afold: 0.643 Carnac(20): 0.597 Sensitivity Afold: 0.632 Carnac(20): 0.400 Positive Predictive Value Afold: 0.659 Carnac(20): 0.898 Number of pairs reference - predicted secondary structure: 163 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs RNASLOpt Matthews Correlation Coefficient Afold: 0.558 RNASLOpt: 0.510 Sensitivity Afold: 0.541 RNASLOpt: 0.460 Positive Predictive Value Afold: 0.582 RNASLOpt: 0.572 Number of pairs reference - predicted secondary structure: 530 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs Cylofold Matthews Correlation Coefficient Afold: 0.582 Cylofold: 0.544 Sensitivity Afold: 0.563 Cylofold: 0.507 Positive Predictive Value Afold: 0.609 Cylofold: 0.591 Number of pairs reference - predicted secondary structure: 479 Wilcoxon single-rank test P-value: 3.56938820447e-08	= Afold vs Multilign(seed) Matthews Correlation Coefficient Afold: 0.482 Multilign(seed): 0.473 Sensitivity Afold: 0.447 Multilign(seed): 0.371 Positive Predictive Value Afold: 0.530 Multilign(seed): 0.613 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 0.00176601553263	+ Afold vs RNAwolf Matthews Correlation Coefficient Afold: 0.558 RNAwolf: 0.509 Sensitivity Afold: 0.541 RNAwolf: 0.507 Positive Predictive Value Afold: 0.582 RNAwolf: 0.518 Number of pairs reference - predicted secondary structure: 530 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs PPfold(seed) Matthews Correlation Coefficient Afold: 0.665 PPfold(seed): 0.472 Sensitivity Afold: 0.649 PPfold(seed): 0.263 Positive Predictive Value Afold: 0.686 PPfold(seed): 0.854 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	+ Afold vs Murlet(seed) Matthews Correlation Coefficient Afold: 0.613 Murlet(seed): 0.481 Sensitivity Afold: 0.596 Murlet(seed): 0.275 Positive Predictive Value Afold: 0.634 Murlet(seed): 0.846 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs Alterna Matthews Correlation Coefficient Afold: 0.542 Alterna: 0.531 Sensitivity Afold: 0.522 Alterna: 0.509 Positive Predictive Value Afold: 0.574 Alterna: 0.565 Number of pairs reference - predicted secondary structure: 402 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ Afold vs Carnac(seed) Matthews Correlation Coefficient Afold: 0.635 Carnac(seed): 0.447 Sensitivity Afold: 0.622 Carnac(seed): 0.227 Positive Predictive Value Afold: 0.653 Carnac(seed): 0.883 Number of pairs reference - predicted secondary structure: 102 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs Vsfold4 Matthews Correlation Coefficient Afold: 0.558 Vsfold4: 0.402 Sensitivity Afold: 0.541 Vsfold4: 0.361 Positive Predictive Value Afold: 0.582 Vsfold4: 0.456 Number of pairs reference - predicted secondary structure: 530 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs RSpredict(seed) Matthews Correlation Coefficient Afold: 0.649 RSpredict(seed): 0.405 Sensitivity Afold: 0.646 RSpredict(seed): 0.283 Positive Predictive Value Afold: 0.657 RSpredict(seed): 0.586 Number of pairs reference - predicted secondary structure: 162 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs Vsfold5 Matthews Correlation Coefficient Afold: 0.558 Vsfold5: 0.403 Sensitivity Afold: 0.541 Vsfold5: 0.370 Positive Predictive Value Afold: 0.582 Vsfold5: 0.447 Number of pairs reference - predicted secondary structure: 530 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs RDfolder Matthews Correlation Coefficient Afold: 0.542 RDfolder: 0.482 Sensitivity Afold: 0.522 RDfolder: 0.417 Positive Predictive Value Afold: 0.574 RDfolder: 0.569 Number of pairs reference - predicted secondary structure: 402 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs MCFold Matthews Correlation Coefficient Afold: 0.556 MCFold: 0.482 Sensitivity Afold: 0.538 MCFold: 0.521 Positive Predictive Value Afold: 0.581 MCFold: 0.454 Number of pairs reference - predicted secondary structure: 472 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs NanoFolder Matthews Correlation Coefficient Afold: 0.550 NanoFolder: 0.320 Sensitivity Afold: 0.536 NanoFolder: 0.361 Positive Predictive Value Afold: 0.570 NanoFolder: 0.293 Number of pairs reference - predicted secondary structure: 72 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Afold vs Mastr(seed) Matthews Correlation Coefficient Afold: 0.641 Mastr(seed): 0.305 Sensitivity Afold: 0.637 Mastr(seed): 0.119 Positive Predictive Value Afold: 0.649 Mastr(seed): 0.787 Number of pairs reference - predicted secondary structure: 167 Wilcoxon single-rank test P-value: 3.56938820447e-08
Pknots	697 ContextFold vs Pknots Matthews Correlation Coefficient ContextFold: 0.763 Pknots: 0.606 Sensitivity ContextFold: 0.721 Pknots: 0.595 Positive Predictive Value ContextFold: 0.811 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	212 TurboFold(20) vs Pknots Matthews Correlation Coefficient TurboFold(20): 0.910 Pknots: 0.655 Sensitivity TurboFold(20): 0.885 Pknots: 0.662 Positive Predictive Value TurboFold(20): 0.937 Pknots: 0.653 Number of pairs reference - predicted secondary structure: 212 Wilcoxon single-rank test P-value: 3.56938820447e-08	146 CentroidAlifold(seed) vs Pknots Matthews Correlation Coefficient CentroidAlifold(seed): 0.780 Pknots: 0.509 Sensitivity CentroidAlifold(seed): 0.673 Pknots: 0.504 Positive Predictive Value CentroidAlifold(seed): 0.906 Pknots: 0.523 Number of pairs reference - predicted secondary structure: 146 Wilcoxon single-rank test P-value: 3.56938820447e-08	697 CentroidHomfold‑LAST vs Pknots Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.745 Pknots: 0.606 Sensitivity CentroidHomfold‑LAST: 0.685 Pknots: 0.595 Positive Predictive Value CentroidHomfold‑LAST: 0.815 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	360 PETfold_pre2.0(seed) vs Pknots Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.909 Pknots: 0.666 Sensitivity PETfold_pre2.0(seed): 0.870 Pknots: 0.673 Positive Predictive Value PETfold_pre2.0(seed): 0.950 Pknots: 0.663 Number of pairs reference - predicted secondary structure: 360 Wilcoxon single-rank test P-value: 3.56938820447e-08	25 TurboFold(seed) vs Pknots Matthews Correlation Coefficient TurboFold(seed): 0.711 Pknots: 0.628 Sensitivity TurboFold(seed): 0.662 Pknots: 0.632 Positive Predictive Value TurboFold(seed): 0.768 Pknots: 0.630 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.10776592382e-08	157 MXScarna(seed) vs Pknots Matthews Correlation Coefficient MXScarna(seed): 0.748 Pknots: 0.532 Sensitivity MXScarna(seed): 0.715 Pknots: 0.527 Positive Predictive Value MXScarna(seed): 0.787 Pknots: 0.545 Number of pairs reference - predicted secondary structure: 157 Wilcoxon single-rank test P-value: 3.56938820447e-08	212 CentroidAlifold(20) vs Pknots Matthews Correlation Coefficient CentroidAlifold(20): 0.906 Pknots: 0.655 Sensitivity CentroidAlifold(20): 0.843 Pknots: 0.662 Positive Predictive Value CentroidAlifold(20): 0.974 Pknots: 0.653 Number of pairs reference - predicted secondary structure: 212 Wilcoxon single-rank test P-value: 3.56938820447e-08	212 PETfold_pre2.0(20) vs Pknots Matthews Correlation Coefficient PETfold_pre2.0(20): 0.885 Pknots: 0.655 Sensitivity PETfold_pre2.0(20): 0.807 Pknots: 0.662 Positive Predictive Value PETfold_pre2.0(20): 0.972 Pknots: 0.653 Number of pairs reference - predicted secondary structure: 212 Wilcoxon single-rank test P-value: 3.56938820447e-08	212 MXScarna(20) vs Pknots Matthews Correlation Coefficient MXScarna(20): 0.872 Pknots: 0.655 Sensitivity MXScarna(20): 0.834 Pknots: 0.662 Positive Predictive Value MXScarna(20): 0.913 Pknots: 0.653 Number of pairs reference - predicted secondary structure: 212 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 PPfold(20) vs Pknots Matthews Correlation Coefficient PPfold(20): 0.882 Pknots: 0.664 Sensitivity PPfold(20): 0.796 Pknots: 0.671 Positive Predictive Value PPfold(20): 0.979 Pknots: 0.662 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	212 RNAalifold(20) vs Pknots Matthews Correlation Coefficient RNAalifold(20): 0.881 Pknots: 0.655 Sensitivity RNAalifold(20): 0.794 Pknots: 0.662 Positive Predictive Value RNAalifold(20): 0.980 Pknots: 0.653 Number of pairs reference - predicted secondary structure: 212 Wilcoxon single-rank test P-value: 3.56938820447e-08	212 RSpredict(20) vs Pknots Matthews Correlation Coefficient RSpredict(20): 0.821 Pknots: 0.655 Sensitivity RSpredict(20): 0.738 Pknots: 0.662 Positive Predictive Value RSpredict(20): 0.915 Pknots: 0.653 Number of pairs reference - predicted secondary structure: 212 Wilcoxon single-rank test P-value: 3.56938820447e-08	697 IPknot vs Pknots Matthews Correlation Coefficient IPknot: 0.687 Pknots: 0.606 Sensitivity IPknot: 0.652 Pknots: 0.595 Positive Predictive Value IPknot: 0.729 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	210 Multilign(20) vs Pknots Matthews Correlation Coefficient Multilign(20): 0.827 Pknots: 0.656 Sensitivity Multilign(20): 0.757 Pknots: 0.662 Positive Predictive Value Multilign(20): 0.906 Pknots: 0.654 Number of pairs reference - predicted secondary structure: 210 Wilcoxon single-rank test P-value: 3.56938820447e-08	697 CentroidFold vs Pknots Matthews Correlation Coefficient CentroidFold: 0.656 Pknots: 0.606 Sensitivity CentroidFold: 0.620 Pknots: 0.595 Positive Predictive Value CentroidFold: 0.701 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	697 Contrafold vs Pknots Matthews Correlation Coefficient Contrafold: 0.656 Pknots: 0.606 Sensitivity Contrafold: 0.645 Pknots: 0.595 Positive Predictive Value Contrafold: 0.673 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 RNASampler(20) vs Pknots Matthews Correlation Coefficient RNASampler(20): 0.857 Pknots: 0.660 Sensitivity RNASampler(20): 0.758 Pknots: 0.666 Positive Predictive Value RNASampler(20): 0.971 Pknots: 0.658 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	211 Murlet(20) vs Pknots Matthews Correlation Coefficient Murlet(20): 0.780 Pknots: 0.657 Sensitivity Murlet(20): 0.685 Pknots: 0.663 Positive Predictive Value Murlet(20): 0.892 Pknots: 0.655 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	62 CMfinder(seed) vs Pknots Matthews Correlation Coefficient CMfinder(seed): 0.512 Pknots: 0.398 Sensitivity CMfinder(seed): 0.382 Pknots: 0.381 Positive Predictive Value CMfinder(seed): 0.696 Pknots: 0.429 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	697 MaxExpect vs Pknots Matthews Correlation Coefficient MaxExpect: 0.640 Pknots: 0.606 Sensitivity MaxExpect: 0.621 Pknots: 0.595 Positive Predictive Value MaxExpect: 0.666 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	212 CMfinder(20) vs Pknots Matthews Correlation Coefficient CMfinder(20): 0.791 Pknots: 0.655 Sensitivity CMfinder(20): 0.678 Pknots: 0.662 Positive Predictive Value CMfinder(20): 0.926 Pknots: 0.653 Number of pairs reference - predicted secondary structure: 212 Wilcoxon single-rank test P-value: 3.56938820447e-08	696 CRWrnafold vs Pknots Matthews Correlation Coefficient CRWrnafold: 0.614 Pknots: 0.606 Sensitivity CRWrnafold: 0.600 Pknots: 0.595 Positive Predictive Value CRWrnafold: 0.634 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 696 Wilcoxon single-rank test P-value: 5.62644058675e-08	697 ProbKnot vs Pknots Matthews Correlation Coefficient ProbKnot: 0.639 Pknots: 0.606 Sensitivity ProbKnot: 0.631 Pknots: 0.595 Positive Predictive Value ProbKnot: 0.655 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	212 Mastr(20) vs Pknots Matthews Correlation Coefficient Mastr(20): 0.727 Pknots: 0.655 Sensitivity Mastr(20): 0.672 Pknots: 0.662 Positive Predictive Value Mastr(20): 0.790 Pknots: 0.653 Number of pairs reference - predicted secondary structure: 212 Wilcoxon single-rank test P-value: 3.56938820447e-08	697 Fold vs Pknots Matthews Correlation Coefficient Fold: 0.633 Pknots: 0.606 Sensitivity Fold: 0.622 Pknots: 0.595 Positive Predictive Value Fold: 0.650 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	697 Pknots vs UNAFold Matthews Correlation Coefficient Pknots: 0.606 UNAFold: 0.596 Sensitivity Pknots: 0.595 UNAFold: 0.583 Positive Predictive Value Pknots: 0.624 UNAFold: 0.616 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	697 Pknots vs PknotsRG Matthews Correlation Coefficient Pknots: 0.606 PknotsRG: 0.603 Sensitivity Pknots: 0.595 PknotsRG: 0.595 Positive Predictive Value Pknots: 0.624 PknotsRG: 0.617 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 8.10048797242e-06	697 Pknots vs Sfold Matthews Correlation Coefficient Pknots: 0.606 Sfold: 0.601 Sensitivity Pknots: 0.595 Sfold: 0.565 Positive Predictive Value Pknots: 0.624 Sfold: 0.648 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 1.70738736246e-07	135 RNAalifold(seed) vs Pknots Matthews Correlation Coefficient RNAalifold(seed): 0.618 Pknots: 0.488 Sensitivity RNAalifold(seed): 0.420 Pknots: 0.481 Positive Predictive Value RNAalifold(seed): 0.914 Pknots: 0.503 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	697 RNAsubopt vs Pknots Matthews Correlation Coefficient RNAsubopt: 0.608 Pknots: 0.606 Sensitivity RNAsubopt: 0.602 Pknots: 0.595 Positive Predictive Value RNAsubopt: 0.620 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 0.00297289556633	697 Pknots vs HotKnots Matthews Correlation Coefficient Pknots: 0.606 HotKnots: 0.593 Sensitivity Pknots: 0.595 HotKnots: 0.589 Positive Predictive Value Pknots: 0.624 HotKnots: 0.604 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	697 Pknots vs RNAfold Matthews Correlation Coefficient Pknots: 0.606 RNAfold: 0.596 Sensitivity Pknots: 0.595 RNAfold: 0.588 Positive Predictive Value Pknots: 0.624 RNAfold: 0.611 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	697 Pknots vs RNAshapes Matthews Correlation Coefficient Pknots: 0.606 RNAshapes: 0.594 Sensitivity Pknots: 0.595 RNAshapes: 0.585 Positive Predictive Value Pknots: 0.624 RNAshapes: 0.610 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	69 RNASampler(seed) vs Pknots Matthews Correlation Coefficient RNASampler(seed): 0.455 Pknots: 0.446 Sensitivity RNASampler(seed): 0.284 Pknots: 0.429 Positive Predictive Value RNASampler(seed): 0.738 Pknots: 0.475 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 5.21379515797e-05	404 Afold vs Pknots Matthews Correlation Coefficient Afold: 0.540 Pknots: 0.537 Sensitivity Afold: 0.519 Pknots: 0.511 Positive Predictive Value Afold: 0.572 Pknots: 0.575 Number of pairs reference - predicted secondary structure: 404 Wilcoxon single-rank test P-value: 0.247700967591		- McQFold vs Pknots Matthews Correlation Coefficient McQFold: 0.650 Pknots: 0.606 Sensitivity McQFold: 0.621 Pknots: 0.595 Positive Predictive Value McQFold: 0.686 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Carnac(20) vs Pknots Matthews Correlation Coefficient Carnac(20): 0.742 Pknots: 0.655 Sensitivity Carnac(20): 0.588 Pknots: 0.662 Positive Predictive Value Carnac(20): 0.940 Pknots: 0.653 Number of pairs reference - predicted secondary structure: 212 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RNASLOpt vs Pknots Matthews Correlation Coefficient RNASLOpt: 0.610 Pknots: 0.606 Sensitivity RNASLOpt: 0.566 Pknots: 0.595 Positive Predictive Value RNASLOpt: 0.665 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 0.000256148526873	- Cylofold vs Pknots Matthews Correlation Coefficient Cylofold: 0.621 Pknots: 0.614 Sensitivity Cylofold: 0.599 Pknots: 0.603 Positive Predictive Value Cylofold: 0.650 Pknots: 0.632 Number of pairs reference - predicted secondary structure: 676 Wilcoxon single-rank test P-value: 3.85233844192e-08	+ Pknots vs Multilign(seed) Matthews Correlation Coefficient Pknots: 0.699 Multilign(seed): 0.485 Sensitivity Pknots: 0.684 Multilign(seed): 0.386 Positive Predictive Value Pknots: 0.721 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.74172190343e-08	+ Pknots vs RNAwolf Matthews Correlation Coefficient Pknots: 0.606 RNAwolf: 0.550 Sensitivity Pknots: 0.595 RNAwolf: 0.554 Positive Predictive Value Pknots: 0.624 RNAwolf: 0.554 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs PPfold(seed) Matthews Correlation Coefficient Pknots: 0.646 PPfold(seed): 0.488 Sensitivity Pknots: 0.645 PPfold(seed): 0.281 Positive Predictive Value Pknots: 0.653 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	= Murlet(seed) vs Pknots Matthews Correlation Coefficient Murlet(seed): 0.451 Pknots: 0.444 Sensitivity Murlet(seed): 0.267 Pknots: 0.428 Positive Predictive Value Murlet(seed): 0.771 Pknots: 0.471 Number of pairs reference - predicted secondary structure: 71 Wilcoxon single-rank test P-value: 0.0239370604239	+ Pknots vs Alterna Matthews Correlation Coefficient Pknots: 0.610 Alterna: 0.552 Sensitivity Pknots: 0.599 Alterna: 0.547 Positive Predictive Value Pknots: 0.629 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Carnac(seed) vs Pknots Matthews Correlation Coefficient Carnac(seed): 0.498 Pknots: 0.484 Sensitivity Carnac(seed): 0.276 Pknots: 0.470 Positive Predictive Value Carnac(seed): 0.907 Pknots: 0.509 Number of pairs reference - predicted secondary structure: 90 Wilcoxon single-rank test P-value: 3.76761760679e-06	+ Pknots vs Vsfold4 Matthews Correlation Coefficient Pknots: 0.606 Vsfold4: 0.592 Sensitivity Pknots: 0.595 Vsfold4: 0.544 Positive Predictive Value Pknots: 0.624 Vsfold4: 0.651 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs RSpredict(seed) Matthews Correlation Coefficient Pknots: 0.509 RSpredict(seed): 0.475 Sensitivity Pknots: 0.504 RSpredict(seed): 0.341 Positive Predictive Value Pknots: 0.523 RSpredict(seed): 0.669 Number of pairs reference - predicted secondary structure: 146 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs Vsfold5 Matthews Correlation Coefficient Pknots: 0.606 Vsfold5: 0.579 Sensitivity Pknots: 0.595 Vsfold5: 0.548 Positive Predictive Value Pknots: 0.624 Vsfold5: 0.620 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs RDfolder Matthews Correlation Coefficient Pknots: 0.610 RDfolder: 0.520 Sensitivity Pknots: 0.599 RDfolder: 0.464 Positive Predictive Value Pknots: 0.629 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs MCFold Matthews Correlation Coefficient Pknots: 0.598 MCFold: 0.466 Sensitivity Pknots: 0.585 MCFold: 0.521 Positive Predictive Value Pknots: 0.620 MCFold: 0.426 Number of pairs reference - predicted secondary structure: 653 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs NanoFolder Matthews Correlation Coefficient Pknots: 0.604 NanoFolder: 0.390 Sensitivity Pknots: 0.590 NanoFolder: 0.447 Positive Predictive Value Pknots: 0.625 NanoFolder: 0.350 Number of pairs reference - predicted secondary structure: 87 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Pknots vs Mastr(seed) Matthews Correlation Coefficient Pknots: 0.533 Mastr(seed): 0.307 Sensitivity Pknots: 0.528 Mastr(seed): 0.117 Positive Predictive Value Pknots: 0.545 Mastr(seed): 0.815 Number of pairs reference - predicted secondary structure: 158 Wilcoxon single-rank test P-value: 3.56938820447e-08
McQFold	882 ContextFold vs McQFold Matthews Correlation Coefficient ContextFold: 0.779 McQFold: 0.583 Sensitivity ContextFold: 0.741 McQFold: 0.557 Positive Predictive Value ContextFold: 0.823 McQFold: 0.616 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 TurboFold(20) vs McQFold Matthews Correlation Coefficient TurboFold(20): 0.889 McQFold: 0.610 Sensitivity TurboFold(20): 0.861 McQFold: 0.587 Positive Predictive Value TurboFold(20): 0.919 McQFold: 0.639 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	216 CentroidAlifold(seed) vs McQFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.790 McQFold: 0.562 Sensitivity CentroidAlifold(seed): 0.699 McQFold: 0.537 Positive Predictive Value CentroidAlifold(seed): 0.896 McQFold: 0.593 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 CentroidHomfold‑LAST vs McQFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.736 McQFold: 0.583 Sensitivity CentroidHomfold‑LAST: 0.665 McQFold: 0.557 Positive Predictive Value CentroidHomfold‑LAST: 0.818 McQFold: 0.616 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	498 PETfold_pre2.0(seed) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.879 McQFold: 0.635 Sensitivity PETfold_pre2.0(seed): 0.825 McQFold: 0.613 Positive Predictive Value PETfold_pre2.0(seed): 0.938 McQFold: 0.662 Number of pairs reference - predicted secondary structure: 498 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 TurboFold(seed) vs McQFold Matthews Correlation Coefficient TurboFold(seed): 0.798 McQFold: 0.623 Sensitivity TurboFold(seed): 0.766 McQFold: 0.600 Positive Predictive Value TurboFold(seed): 0.835 McQFold: 0.652 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	233 MXScarna(seed) vs McQFold Matthews Correlation Coefficient MXScarna(seed): 0.750 McQFold: 0.564 Sensitivity MXScarna(seed): 0.712 McQFold: 0.540 Positive Predictive Value MXScarna(seed): 0.793 McQFold: 0.595 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 CentroidAlifold(20) vs McQFold Matthews Correlation Coefficient CentroidAlifold(20): 0.849 McQFold: 0.610 Sensitivity CentroidAlifold(20): 0.754 McQFold: 0.587 Positive Predictive Value CentroidAlifold(20): 0.957 McQFold: 0.639 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 PETfold_pre2.0(20) vs McQFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 McQFold: 0.610 Sensitivity PETfold_pre2.0(20): 0.737 McQFold: 0.587 Positive Predictive Value PETfold_pre2.0(20): 0.975 McQFold: 0.639 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 MXScarna(20) vs McQFold Matthews Correlation Coefficient MXScarna(20): 0.838 McQFold: 0.610 Sensitivity MXScarna(20): 0.791 McQFold: 0.587 Positive Predictive Value MXScarna(20): 0.891 McQFold: 0.639 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	314 PPfold(20) vs McQFold Matthews Correlation Coefficient PPfold(20): 0.839 McQFold: 0.613 Sensitivity PPfold(20): 0.721 McQFold: 0.590 Positive Predictive Value PPfold(20): 0.977 McQFold: 0.642 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RNAalifold(20) vs McQFold Matthews Correlation Coefficient RNAalifold(20): 0.816 McQFold: 0.610 Sensitivity RNAalifold(20): 0.690 McQFold: 0.587 Positive Predictive Value RNAalifold(20): 0.966 McQFold: 0.639 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RSpredict(20) vs McQFold Matthews Correlation Coefficient RSpredict(20): 0.789 McQFold: 0.610 Sensitivity RSpredict(20): 0.693 McQFold: 0.587 Positive Predictive Value RSpredict(20): 0.901 McQFold: 0.639 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 IPknot vs McQFold Matthews Correlation Coefficient IPknot: 0.694 McQFold: 0.583 Sensitivity IPknot: 0.661 McQFold: 0.557 Positive Predictive Value IPknot: 0.733 McQFold: 0.616 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	311 Multilign(20) vs McQFold Matthews Correlation Coefficient Multilign(20): 0.784 McQFold: 0.614 Sensitivity Multilign(20): 0.697 McQFold: 0.591 Positive Predictive Value Multilign(20): 0.885 McQFold: 0.643 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 CentroidFold vs McQFold Matthews Correlation Coefficient CentroidFold: 0.645 McQFold: 0.583 Sensitivity CentroidFold: 0.612 McQFold: 0.557 Positive Predictive Value CentroidFold: 0.684 McQFold: 0.616 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 Contrafold vs McQFold Matthews Correlation Coefficient Contrafold: 0.643 McQFold: 0.583 Sensitivity Contrafold: 0.634 McQFold: 0.557 Positive Predictive Value Contrafold: 0.657 McQFold: 0.616 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	315 RNASampler(20) vs McQFold Matthews Correlation Coefficient RNASampler(20): 0.770 McQFold: 0.613 Sensitivity RNASampler(20): 0.622 McQFold: 0.589 Positive Predictive Value RNASampler(20): 0.957 McQFold: 0.643 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	319 Murlet(20) vs McQFold Matthews Correlation Coefficient Murlet(20): 0.750 McQFold: 0.612 Sensitivity Murlet(20): 0.619 McQFold: 0.589 Positive Predictive Value Murlet(20): 0.913 McQFold: 0.641 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 CMfinder(seed) vs McQFold Matthews Correlation Coefficient CMfinder(seed): 0.571 McQFold: 0.536 Sensitivity CMfinder(seed): 0.439 McQFold: 0.489 Positive Predictive Value CMfinder(seed): 0.747 McQFold: 0.593 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 MaxExpect vs McQFold Matthews Correlation Coefficient MaxExpect: 0.633 McQFold: 0.583 Sensitivity MaxExpect: 0.617 McQFold: 0.557 Positive Predictive Value MaxExpect: 0.654 McQFold: 0.616 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	316 CMfinder(20) vs McQFold Matthews Correlation Coefficient CMfinder(20): 0.735 McQFold: 0.611 Sensitivity CMfinder(20): 0.603 McQFold: 0.588 Positive Predictive Value CMfinder(20): 0.899 McQFold: 0.639 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	881 CRWrnafold vs McQFold Matthews Correlation Coefficient CRWrnafold: 0.630 McQFold: 0.583 Sensitivity CRWrnafold: 0.618 McQFold: 0.557 Positive Predictive Value CRWrnafold: 0.648 McQFold: 0.616 Number of pairs reference - predicted secondary structure: 881 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 ProbKnot vs McQFold Matthews Correlation Coefficient ProbKnot: 0.630 McQFold: 0.583 Sensitivity ProbKnot: 0.622 McQFold: 0.557 Positive Predictive Value ProbKnot: 0.644 McQFold: 0.616 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 Mastr(20) vs McQFold Matthews Correlation Coefficient Mastr(20): 0.708 McQFold: 0.610 Sensitivity Mastr(20): 0.635 McQFold: 0.587 Positive Predictive Value Mastr(20): 0.793 McQFold: 0.639 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 Fold vs McQFold Matthews Correlation Coefficient Fold: 0.628 McQFold: 0.583 Sensitivity Fold: 0.620 McQFold: 0.557 Positive Predictive Value Fold: 0.641 McQFold: 0.616 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 UNAFold vs McQFold Matthews Correlation Coefficient UNAFold: 0.620 McQFold: 0.583 Sensitivity UNAFold: 0.605 McQFold: 0.557 Positive Predictive Value UNAFold: 0.639 McQFold: 0.616 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 PknotsRG vs McQFold Matthews Correlation Coefficient PknotsRG: 0.617 McQFold: 0.583 Sensitivity PknotsRG: 0.610 McQFold: 0.557 Positive Predictive Value PknotsRG: 0.630 McQFold: 0.616 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 Sfold vs McQFold Matthews Correlation Coefficient Sfold: 0.618 McQFold: 0.583 Sensitivity Sfold: 0.581 McQFold: 0.557 Positive Predictive Value Sfold: 0.663 McQFold: 0.616 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	205 RNAalifold(seed) vs McQFold Matthews Correlation Coefficient RNAalifold(seed): 0.610 McQFold: 0.550 Sensitivity RNAalifold(seed): 0.404 McQFold: 0.524 Positive Predictive Value RNAalifold(seed): 0.923 McQFold: 0.583 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 RNAsubopt vs McQFold Matthews Correlation Coefficient RNAsubopt: 0.615 McQFold: 0.583 Sensitivity RNAsubopt: 0.609 McQFold: 0.557 Positive Predictive Value RNAsubopt: 0.626 McQFold: 0.616 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	875 HotKnots vs McQFold Matthews Correlation Coefficient HotKnots: 0.613 McQFold: 0.583 Sensitivity HotKnots: 0.607 McQFold: 0.558 Positive Predictive Value HotKnots: 0.624 McQFold: 0.616 Number of pairs reference - predicted secondary structure: 875 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 RNAfold vs McQFold Matthews Correlation Coefficient RNAfold: 0.612 McQFold: 0.583 Sensitivity RNAfold: 0.604 McQFold: 0.557 Positive Predictive Value RNAfold: 0.626 McQFold: 0.616 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 RNAshapes vs McQFold Matthews Correlation Coefficient RNAshapes: 0.612 McQFold: 0.583 Sensitivity RNAshapes: 0.602 McQFold: 0.557 Positive Predictive Value RNAshapes: 0.628 McQFold: 0.616 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	86 McQFold vs RNASampler(seed) Matthews Correlation Coefficient McQFold: 0.560 RNASampler(seed): 0.557 Sensitivity McQFold: 0.514 RNASampler(seed): 0.389 Positive Predictive Value McQFold: 0.614 RNASampler(seed): 0.802 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 0.192299791283	530 Afold vs McQFold Matthews Correlation Coefficient Afold: 0.558 McQFold: 0.534 Sensitivity Afold: 0.541 McQFold: 0.501 Positive Predictive Value Afold: 0.582 McQFold: 0.576 Number of pairs reference - predicted secondary structure: 530 Wilcoxon single-rank test P-value: 3.56938820447e-08	697 McQFold vs Pknots Matthews Correlation Coefficient McQFold: 0.650 Pknots: 0.606 Sensitivity McQFold: 0.621 Pknots: 0.595 Positive Predictive Value McQFold: 0.686 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08		- Carnac(20) vs McQFold Matthews Correlation Coefficient Carnac(20): 0.675 McQFold: 0.610 Sensitivity Carnac(20): 0.500 McQFold: 0.587 Positive Predictive Value Carnac(20): 0.915 McQFold: 0.639 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs RNASLOpt Matthews Correlation Coefficient McQFold: 0.583 RNASLOpt: 0.562 Sensitivity McQFold: 0.557 RNASLOpt: 0.521 Positive Predictive Value McQFold: 0.616 RNASLOpt: 0.613 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Cylofold Matthews Correlation Coefficient McQFold: 0.617 Cylofold: 0.577 Sensitivity McQFold: 0.587 Cylofold: 0.554 Positive Predictive Value McQFold: 0.654 Cylofold: 0.608 Number of pairs reference - predicted secondary structure: 796 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Multilign(seed) Matthews Correlation Coefficient McQFold: 0.765 Multilign(seed): 0.485 Sensitivity McQFold: 0.730 Multilign(seed): 0.386 Positive Predictive Value McQFold: 0.805 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.24270395587e-08	+ McQFold vs RNAwolf Matthews Correlation Coefficient McQFold: 0.583 RNAwolf: 0.518 Sensitivity McQFold: 0.557 RNAwolf: 0.523 Positive Predictive Value McQFold: 0.616 RNAwolf: 0.520 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs PPfold(seed) Matthews Correlation Coefficient McQFold: 0.672 PPfold(seed): 0.380 Sensitivity McQFold: 0.651 PPfold(seed): 0.170 Positive Predictive Value McQFold: 0.697 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Murlet(seed) Matthews Correlation Coefficient McQFold: 0.561 Murlet(seed): 0.468 Sensitivity McQFold: 0.518 Murlet(seed): 0.266 Positive Predictive Value McQFold: 0.612 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Alterna Matthews Correlation Coefficient McQFold: 0.653 Alterna: 0.552 Sensitivity McQFold: 0.624 Alterna: 0.547 Positive Predictive Value McQFold: 0.689 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Carnac(seed) Matthews Correlation Coefficient McQFold: 0.581 Carnac(seed): 0.415 Sensitivity McQFold: 0.545 Carnac(seed): 0.196 Positive Predictive Value McQFold: 0.624 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Vsfold4 Matthews Correlation Coefficient McQFold: 0.583 Vsfold4: 0.487 Sensitivity McQFold: 0.557 Vsfold4: 0.447 Positive Predictive Value McQFold: 0.616 Vsfold4: 0.537 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs RSpredict(seed) Matthews Correlation Coefficient McQFold: 0.562 RSpredict(seed): 0.373 Sensitivity McQFold: 0.537 RSpredict(seed): 0.251 Positive Predictive Value McQFold: 0.593 RSpredict(seed): 0.562 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Vsfold5 Matthews Correlation Coefficient McQFold: 0.583 Vsfold5: 0.477 Sensitivity McQFold: 0.557 Vsfold5: 0.450 Positive Predictive Value McQFold: 0.616 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs RDfolder Matthews Correlation Coefficient McQFold: 0.653 RDfolder: 0.520 Sensitivity McQFold: 0.624 RDfolder: 0.464 Positive Predictive Value McQFold: 0.689 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs MCFold Matthews Correlation Coefficient McQFold: 0.593 MCFold: 0.473 Sensitivity McQFold: 0.563 MCFold: 0.524 Positive Predictive Value McQFold: 0.631 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs NanoFolder Matthews Correlation Coefficient McQFold: 0.589 NanoFolder: 0.335 Sensitivity McQFold: 0.559 NanoFolder: 0.384 Positive Predictive Value McQFold: 0.626 NanoFolder: 0.301 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ McQFold vs Mastr(seed) Matthews Correlation Coefficient McQFold: 0.565 Mastr(seed): 0.263 Sensitivity McQFold: 0.541 Mastr(seed): 0.089 Positive Predictive Value McQFold: 0.595 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08
Carnac(20)	320 ContextFold vs Carnac(20) Matthews Correlation Coefficient ContextFold: 0.923 Carnac(20): 0.675 Sensitivity ContextFold: 0.898 Carnac(20): 0.500 Positive Predictive Value ContextFold: 0.949 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 TurboFold(20) vs Carnac(20) Matthews Correlation Coefficient TurboFold(20): 0.889 Carnac(20): 0.675 Sensitivity TurboFold(20): 0.861 Carnac(20): 0.500 Positive Predictive Value TurboFold(20): 0.919 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	141 CentroidAlifold(seed) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(seed): 0.815 Carnac(20): 0.467 Sensitivity CentroidAlifold(seed): 0.743 Carnac(20): 0.260 Positive Predictive Value CentroidAlifold(seed): 0.897 Carnac(20): 0.845 Number of pairs reference - predicted secondary structure: 141 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 CentroidHomfold‑LAST vs Carnac(20) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.858 Carnac(20): 0.675 Sensitivity CentroidHomfold‑LAST: 0.821 Carnac(20): 0.500 Positive Predictive Value CentroidHomfold‑LAST: 0.900 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	319 PETfold_pre2.0(seed) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.885 Carnac(20): 0.676 Sensitivity PETfold_pre2.0(seed): 0.832 Carnac(20): 0.501 Positive Predictive Value PETfold_pre2.0(seed): 0.944 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 TurboFold(seed) vs Carnac(20) Matthews Correlation Coefficient TurboFold(seed): 0.880 Carnac(20): 0.511 Sensitivity TurboFold(seed): 0.875 Carnac(20): 0.314 Positive Predictive Value TurboFold(seed): 0.886 Carnac(20): 0.837 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 1.87872347734e-08	153 MXScarna(seed) vs Carnac(20) Matthews Correlation Coefficient MXScarna(seed): 0.792 Carnac(20): 0.510 Sensitivity MXScarna(seed): 0.756 Carnac(20): 0.302 Positive Predictive Value MXScarna(seed): 0.832 Carnac(20): 0.867 Number of pairs reference - predicted secondary structure: 153 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 CentroidAlifold(20) vs Carnac(20) Matthews Correlation Coefficient CentroidAlifold(20): 0.849 Carnac(20): 0.675 Sensitivity CentroidAlifold(20): 0.754 Carnac(20): 0.500 Positive Predictive Value CentroidAlifold(20): 0.957 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 PETfold_pre2.0(20) vs Carnac(20) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 Carnac(20): 0.675 Sensitivity PETfold_pre2.0(20): 0.737 Carnac(20): 0.500 Positive Predictive Value PETfold_pre2.0(20): 0.975 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 MXScarna(20) vs Carnac(20) Matthews Correlation Coefficient MXScarna(20): 0.838 Carnac(20): 0.675 Sensitivity MXScarna(20): 0.791 Carnac(20): 0.500 Positive Predictive Value MXScarna(20): 0.891 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	314 PPfold(20) vs Carnac(20) Matthews Correlation Coefficient PPfold(20): 0.839 Carnac(20): 0.682 Sensitivity PPfold(20): 0.721 Carnac(20): 0.507 Positive Predictive Value PPfold(20): 0.977 Carnac(20): 0.921 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RNAalifold(20) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(20): 0.816 Carnac(20): 0.675 Sensitivity RNAalifold(20): 0.690 Carnac(20): 0.500 Positive Predictive Value RNAalifold(20): 0.966 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RSpredict(20) vs Carnac(20) Matthews Correlation Coefficient RSpredict(20): 0.789 Carnac(20): 0.675 Sensitivity RSpredict(20): 0.693 Carnac(20): 0.500 Positive Predictive Value RSpredict(20): 0.901 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 IPknot vs Carnac(20) Matthews Correlation Coefficient IPknot: 0.783 Carnac(20): 0.675 Sensitivity IPknot: 0.761 Carnac(20): 0.500 Positive Predictive Value IPknot: 0.807 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	311 Multilign(20) vs Carnac(20) Matthews Correlation Coefficient Multilign(20): 0.784 Carnac(20): 0.683 Sensitivity Multilign(20): 0.697 Carnac(20): 0.511 Positive Predictive Value Multilign(20): 0.885 Carnac(20): 0.916 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 CentroidFold vs Carnac(20) Matthews Correlation Coefficient CentroidFold: 0.735 Carnac(20): 0.675 Sensitivity CentroidFold: 0.710 Carnac(20): 0.500 Positive Predictive Value CentroidFold: 0.764 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 Contrafold vs Carnac(20) Matthews Correlation Coefficient Contrafold: 0.733 Carnac(20): 0.675 Sensitivity Contrafold: 0.729 Carnac(20): 0.500 Positive Predictive Value Contrafold: 0.740 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	315 RNASampler(20) vs Carnac(20) Matthews Correlation Coefficient RNASampler(20): 0.770 Carnac(20): 0.678 Sensitivity RNASampler(20): 0.622 Carnac(20): 0.504 Positive Predictive Value RNASampler(20): 0.957 Carnac(20): 0.916 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	319 Murlet(20) vs Carnac(20) Matthews Correlation Coefficient Murlet(20): 0.750 Carnac(20): 0.676 Sensitivity Murlet(20): 0.619 Carnac(20): 0.501 Positive Predictive Value Murlet(20): 0.913 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 CMfinder(seed) vs Carnac(20) Matthews Correlation Coefficient CMfinder(seed): 0.736 Carnac(20): 0.413 Sensitivity CMfinder(seed): 0.607 Carnac(20): 0.190 Positive Predictive Value CMfinder(seed): 0.898 Carnac(20): 0.911 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 4.39131584674e-08	320 MaxExpect vs Carnac(20) Matthews Correlation Coefficient MaxExpect: 0.711 Carnac(20): 0.675 Sensitivity MaxExpect: 0.701 Carnac(20): 0.500 Positive Predictive Value MaxExpect: 0.725 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	316 CMfinder(20) vs Carnac(20) Matthews Correlation Coefficient CMfinder(20): 0.735 Carnac(20): 0.681 Sensitivity CMfinder(20): 0.603 Carnac(20): 0.508 Positive Predictive Value CMfinder(20): 0.899 Carnac(20): 0.917 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 CRWrnafold vs Carnac(20) Matthews Correlation Coefficient CRWrnafold: 0.783 Carnac(20): 0.675 Sensitivity CRWrnafold: 0.771 Carnac(20): 0.500 Positive Predictive Value CRWrnafold: 0.798 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 ProbKnot vs Carnac(20) Matthews Correlation Coefficient ProbKnot: 0.707 Carnac(20): 0.675 Sensitivity ProbKnot: 0.702 Carnac(20): 0.500 Positive Predictive Value ProbKnot: 0.716 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 Mastr(20) vs Carnac(20) Matthews Correlation Coefficient Mastr(20): 0.708 Carnac(20): 0.675 Sensitivity Mastr(20): 0.635 Carnac(20): 0.500 Positive Predictive Value Mastr(20): 0.793 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 Fold vs Carnac(20) Matthews Correlation Coefficient Fold: 0.712 Carnac(20): 0.675 Sensitivity Fold: 0.710 Carnac(20): 0.500 Positive Predictive Value Fold: 0.717 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 UNAFold vs Carnac(20) Matthews Correlation Coefficient UNAFold: 0.708 Carnac(20): 0.675 Sensitivity UNAFold: 0.696 Carnac(20): 0.500 Positive Predictive Value UNAFold: 0.723 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 PknotsRG vs Carnac(20) Matthews Correlation Coefficient PknotsRG: 0.691 Carnac(20): 0.675 Sensitivity PknotsRG: 0.687 Carnac(20): 0.500 Positive Predictive Value PknotsRG: 0.699 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.85233844192e-08	320 Sfold vs Carnac(20) Matthews Correlation Coefficient Sfold: 0.698 Carnac(20): 0.675 Sensitivity Sfold: 0.662 Carnac(20): 0.500 Positive Predictive Value Sfold: 0.740 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	137 RNAalifold(seed) vs Carnac(20) Matthews Correlation Coefficient RNAalifold(seed): 0.604 Carnac(20): 0.455 Sensitivity RNAalifold(seed): 0.383 Carnac(20): 0.248 Positive Predictive Value RNAalifold(seed): 0.956 Carnac(20): 0.840 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RNAsubopt vs Carnac(20) Matthews Correlation Coefficient RNAsubopt: 0.694 Carnac(20): 0.675 Sensitivity RNAsubopt: 0.693 Carnac(20): 0.500 Positive Predictive Value RNAsubopt: 0.700 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 HotKnots vs Carnac(20) Matthews Correlation Coefficient HotKnots: 0.698 Carnac(20): 0.675 Sensitivity HotKnots: 0.695 Carnac(20): 0.500 Positive Predictive Value HotKnots: 0.705 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RNAfold vs Carnac(20) Matthews Correlation Coefficient RNAfold: 0.686 Carnac(20): 0.675 Sensitivity RNAfold: 0.681 Carnac(20): 0.500 Positive Predictive Value RNAfold: 0.695 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 9.49173053431e-08	320 RNAshapes vs Carnac(20) Matthews Correlation Coefficient RNAshapes: 0.693 Carnac(20): 0.675 Sensitivity RNAshapes: 0.687 Carnac(20): 0.500 Positive Predictive Value RNAshapes: 0.702 Carnac(20): 0.915 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	42 RNASampler(seed) vs Carnac(20) Matthews Correlation Coefficient RNASampler(seed): 0.571 Carnac(20): 0.461 Sensitivity RNASampler(seed): 0.343 Carnac(20): 0.241 Positive Predictive Value RNASampler(seed): 0.957 Carnac(20): 0.893 Number of pairs reference - predicted secondary structure: 42 Wilcoxon single-rank test P-value: 3.56938820447e-08	163 Afold vs Carnac(20) Matthews Correlation Coefficient Afold: 0.643 Carnac(20): 0.597 Sensitivity Afold: 0.632 Carnac(20): 0.400 Positive Predictive Value Afold: 0.659 Carnac(20): 0.898 Number of pairs reference - predicted secondary structure: 163 Wilcoxon single-rank test P-value: 3.56938820447e-08	212 Carnac(20) vs Pknots Matthews Correlation Coefficient Carnac(20): 0.742 Pknots: 0.655 Sensitivity Carnac(20): 0.588 Pknots: 0.662 Positive Predictive Value Carnac(20): 0.940 Pknots: 0.653 Number of pairs reference - predicted secondary structure: 212 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 Carnac(20) vs McQFold Matthews Correlation Coefficient Carnac(20): 0.675 McQFold: 0.610 Sensitivity Carnac(20): 0.500 McQFold: 0.587 Positive Predictive Value Carnac(20): 0.915 McQFold: 0.639 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ Carnac(20) vs RNASLOpt Matthews Correlation Coefficient Carnac(20): 0.675 RNASLOpt: 0.638 Sensitivity Carnac(20): 0.500 RNASLOpt: 0.594 Positive Predictive Value Carnac(20): 0.915 RNASLOpt: 0.690 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs Cylofold Matthews Correlation Coefficient Carnac(20): 0.676 Cylofold: 0.557 Sensitivity Carnac(20): 0.499 Cylofold: 0.543 Positive Predictive Value Carnac(20): 0.918 Cylofold: 0.577 Number of pairs reference - predicted secondary structure: 304 Wilcoxon single-rank test P-value: 3.56938820447e-08	? Carnac(20) vs Multilign(seed) Matthews Correlation Coefficient Carnac(20): 0.588 Multilign(seed): 0.334 Sensitivity Carnac(20): 0.349 Multilign(seed): 0.186 Positive Predictive Value Carnac(20): 1.000 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	+ Carnac(20) vs RNAwolf Matthews Correlation Coefficient Carnac(20): 0.675 RNAwolf: 0.561 Sensitivity Carnac(20): 0.500 RNAwolf: 0.565 Positive Predictive Value Carnac(20): 0.915 RNAwolf: 0.561 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs PPfold(seed) Matthews Correlation Coefficient Carnac(20): 0.496 PPfold(seed): 0.344 Sensitivity Carnac(20): 0.287 PPfold(seed): 0.128 Positive Predictive Value Carnac(20): 0.863 PPfold(seed): 0.927 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 4.94031556815e-08	- Murlet(seed) vs Carnac(20) Matthews Correlation Coefficient Murlet(seed): 0.636 Carnac(20): 0.446 Sensitivity Murlet(seed): 0.428 Carnac(20): 0.224 Positive Predictive Value Murlet(seed): 0.952 Carnac(20): 0.896 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs Alterna Matthews Correlation Coefficient Carnac(20): 0.744 Alterna: 0.618 Sensitivity Carnac(20): 0.591 Alterna: 0.626 Positive Predictive Value Carnac(20): 0.940 Alterna: 0.616 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs Carnac(seed) Matthews Correlation Coefficient Carnac(20): 0.523 Carnac(seed): 0.431 Sensitivity Carnac(20): 0.304 Carnac(seed): 0.206 Positive Predictive Value Carnac(20): 0.905 Carnac(seed): 0.907 Number of pairs reference - predicted secondary structure: 68 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs Vsfold4 Matthews Correlation Coefficient Carnac(20): 0.675 Vsfold4: 0.502 Sensitivity Carnac(20): 0.500 Vsfold4: 0.466 Positive Predictive Value Carnac(20): 0.915 Vsfold4: 0.546 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs RSpredict(seed) Matthews Correlation Coefficient Carnac(20): 0.467 RSpredict(seed): 0.414 Sensitivity Carnac(20): 0.260 RSpredict(seed): 0.279 Positive Predictive Value Carnac(20): 0.845 RSpredict(seed): 0.622 Number of pairs reference - predicted secondary structure: 141 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs Vsfold5 Matthews Correlation Coefficient Carnac(20): 0.675 Vsfold5: 0.457 Sensitivity Carnac(20): 0.500 Vsfold5: 0.437 Positive Predictive Value Carnac(20): 0.915 Vsfold5: 0.484 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs RDfolder Matthews Correlation Coefficient Carnac(20): 0.744 RDfolder: 0.556 Sensitivity Carnac(20): 0.591 RDfolder: 0.511 Positive Predictive Value Carnac(20): 0.940 RDfolder: 0.611 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs MCFold Matthews Correlation Coefficient Carnac(20): 0.677 MCFold: 0.500 Sensitivity Carnac(20): 0.505 MCFold: 0.559 Positive Predictive Value Carnac(20): 0.912 MCFold: 0.453 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs NanoFolder Matthews Correlation Coefficient Carnac(20): 0.668 NanoFolder: 0.337 Sensitivity Carnac(20): 0.492 NanoFolder: 0.391 Positive Predictive Value Carnac(20): 0.910 NanoFolder: 0.298 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(20) vs Mastr(seed) Matthews Correlation Coefficient Carnac(20): 0.512 Mastr(seed): 0.265 Sensitivity Carnac(20): 0.304 Mastr(seed): 0.087 Positive Predictive Value Carnac(20): 0.866 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 154 Wilcoxon single-rank test P-value: 3.56938820447e-08
RNASLOpt	882 ContextFold vs RNASLOpt Matthews Correlation Coefficient ContextFold: 0.779 RNASLOpt: 0.562 Sensitivity ContextFold: 0.741 RNASLOpt: 0.521 Positive Predictive Value ContextFold: 0.823 RNASLOpt: 0.613 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 TurboFold(20) vs RNASLOpt Matthews Correlation Coefficient TurboFold(20): 0.889 RNASLOpt: 0.638 Sensitivity TurboFold(20): 0.861 RNASLOpt: 0.594 Positive Predictive Value TurboFold(20): 0.919 RNASLOpt: 0.690 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	216 CentroidAlifold(seed) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(seed): 0.790 RNASLOpt: 0.579 Sensitivity CentroidAlifold(seed): 0.699 RNASLOpt: 0.530 Positive Predictive Value CentroidAlifold(seed): 0.896 RNASLOpt: 0.638 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 CentroidHomfold‑LAST vs RNASLOpt Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.736 RNASLOpt: 0.562 Sensitivity CentroidHomfold‑LAST: 0.665 RNASLOpt: 0.521 Positive Predictive Value CentroidHomfold‑LAST: 0.818 RNASLOpt: 0.613 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	498 PETfold_pre2.0(seed) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.879 RNASLOpt: 0.630 Sensitivity PETfold_pre2.0(seed): 0.825 RNASLOpt: 0.590 Positive Predictive Value PETfold_pre2.0(seed): 0.938 RNASLOpt: 0.678 Number of pairs reference - predicted secondary structure: 498 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 TurboFold(seed) vs RNASLOpt Matthews Correlation Coefficient TurboFold(seed): 0.798 RNASLOpt: 0.636 Sensitivity TurboFold(seed): 0.766 RNASLOpt: 0.571 Positive Predictive Value TurboFold(seed): 0.835 RNASLOpt: 0.714 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	233 MXScarna(seed) vs RNASLOpt Matthews Correlation Coefficient MXScarna(seed): 0.750 RNASLOpt: 0.574 Sensitivity MXScarna(seed): 0.712 RNASLOpt: 0.526 Positive Predictive Value MXScarna(seed): 0.793 RNASLOpt: 0.630 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 CentroidAlifold(20) vs RNASLOpt Matthews Correlation Coefficient CentroidAlifold(20): 0.849 RNASLOpt: 0.638 Sensitivity CentroidAlifold(20): 0.754 RNASLOpt: 0.594 Positive Predictive Value CentroidAlifold(20): 0.957 RNASLOpt: 0.690 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 PETfold_pre2.0(20) vs RNASLOpt Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 RNASLOpt: 0.638 Sensitivity PETfold_pre2.0(20): 0.737 RNASLOpt: 0.594 Positive Predictive Value PETfold_pre2.0(20): 0.975 RNASLOpt: 0.690 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 MXScarna(20) vs RNASLOpt Matthews Correlation Coefficient MXScarna(20): 0.838 RNASLOpt: 0.638 Sensitivity MXScarna(20): 0.791 RNASLOpt: 0.594 Positive Predictive Value MXScarna(20): 0.891 RNASLOpt: 0.690 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	314 PPfold(20) vs RNASLOpt Matthews Correlation Coefficient PPfold(20): 0.839 RNASLOpt: 0.641 Sensitivity PPfold(20): 0.721 RNASLOpt: 0.596 Positive Predictive Value PPfold(20): 0.977 RNASLOpt: 0.693 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RNAalifold(20) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(20): 0.816 RNASLOpt: 0.638 Sensitivity RNAalifold(20): 0.690 RNASLOpt: 0.594 Positive Predictive Value RNAalifold(20): 0.966 RNASLOpt: 0.690 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RSpredict(20) vs RNASLOpt Matthews Correlation Coefficient RSpredict(20): 0.789 RNASLOpt: 0.638 Sensitivity RSpredict(20): 0.693 RNASLOpt: 0.594 Positive Predictive Value RSpredict(20): 0.901 RNASLOpt: 0.690 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 IPknot vs RNASLOpt Matthews Correlation Coefficient IPknot: 0.694 RNASLOpt: 0.562 Sensitivity IPknot: 0.661 RNASLOpt: 0.521 Positive Predictive Value IPknot: 0.733 RNASLOpt: 0.613 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	311 Multilign(20) vs RNASLOpt Matthews Correlation Coefficient Multilign(20): 0.784 RNASLOpt: 0.640 Sensitivity Multilign(20): 0.697 RNASLOpt: 0.596 Positive Predictive Value Multilign(20): 0.885 RNASLOpt: 0.692 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 CentroidFold vs RNASLOpt Matthews Correlation Coefficient CentroidFold: 0.645 RNASLOpt: 0.562 Sensitivity CentroidFold: 0.612 RNASLOpt: 0.521 Positive Predictive Value CentroidFold: 0.684 RNASLOpt: 0.613 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 Contrafold vs RNASLOpt Matthews Correlation Coefficient Contrafold: 0.643 RNASLOpt: 0.562 Sensitivity Contrafold: 0.634 RNASLOpt: 0.521 Positive Predictive Value Contrafold: 0.657 RNASLOpt: 0.613 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	315 RNASampler(20) vs RNASLOpt Matthews Correlation Coefficient RNASampler(20): 0.770 RNASLOpt: 0.641 Sensitivity RNASampler(20): 0.622 RNASLOpt: 0.596 Positive Predictive Value RNASampler(20): 0.957 RNASLOpt: 0.693 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	319 Murlet(20) vs RNASLOpt Matthews Correlation Coefficient Murlet(20): 0.750 RNASLOpt: 0.640 Sensitivity Murlet(20): 0.619 RNASLOpt: 0.595 Positive Predictive Value Murlet(20): 0.913 RNASLOpt: 0.692 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 CMfinder(seed) vs RNASLOpt Matthews Correlation Coefficient CMfinder(seed): 0.571 RNASLOpt: 0.504 Sensitivity CMfinder(seed): 0.439 RNASLOpt: 0.440 Positive Predictive Value CMfinder(seed): 0.747 RNASLOpt: 0.582 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 MaxExpect vs RNASLOpt Matthews Correlation Coefficient MaxExpect: 0.633 RNASLOpt: 0.562 Sensitivity MaxExpect: 0.617 RNASLOpt: 0.521 Positive Predictive Value MaxExpect: 0.654 RNASLOpt: 0.613 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	316 CMfinder(20) vs RNASLOpt Matthews Correlation Coefficient CMfinder(20): 0.735 RNASLOpt: 0.638 Sensitivity CMfinder(20): 0.603 RNASLOpt: 0.594 Positive Predictive Value CMfinder(20): 0.899 RNASLOpt: 0.690 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	881 CRWrnafold vs RNASLOpt Matthews Correlation Coefficient CRWrnafold: 0.630 RNASLOpt: 0.562 Sensitivity CRWrnafold: 0.618 RNASLOpt: 0.521 Positive Predictive Value CRWrnafold: 0.648 RNASLOpt: 0.613 Number of pairs reference - predicted secondary structure: 881 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 ProbKnot vs RNASLOpt Matthews Correlation Coefficient ProbKnot: 0.630 RNASLOpt: 0.562 Sensitivity ProbKnot: 0.622 RNASLOpt: 0.521 Positive Predictive Value ProbKnot: 0.644 RNASLOpt: 0.613 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 Mastr(20) vs RNASLOpt Matthews Correlation Coefficient Mastr(20): 0.708 RNASLOpt: 0.638 Sensitivity Mastr(20): 0.635 RNASLOpt: 0.594 Positive Predictive Value Mastr(20): 0.793 RNASLOpt: 0.690 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 Fold vs RNASLOpt Matthews Correlation Coefficient Fold: 0.628 RNASLOpt: 0.562 Sensitivity Fold: 0.620 RNASLOpt: 0.521 Positive Predictive Value Fold: 0.641 RNASLOpt: 0.613 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 UNAFold vs RNASLOpt Matthews Correlation Coefficient UNAFold: 0.620 RNASLOpt: 0.562 Sensitivity UNAFold: 0.605 RNASLOpt: 0.521 Positive Predictive Value UNAFold: 0.639 RNASLOpt: 0.613 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 PknotsRG vs RNASLOpt Matthews Correlation Coefficient PknotsRG: 0.617 RNASLOpt: 0.562 Sensitivity PknotsRG: 0.610 RNASLOpt: 0.521 Positive Predictive Value PknotsRG: 0.630 RNASLOpt: 0.613 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 Sfold vs RNASLOpt Matthews Correlation Coefficient Sfold: 0.618 RNASLOpt: 0.562 Sensitivity Sfold: 0.581 RNASLOpt: 0.521 Positive Predictive Value Sfold: 0.663 RNASLOpt: 0.613 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	205 RNAalifold(seed) vs RNASLOpt Matthews Correlation Coefficient RNAalifold(seed): 0.610 RNASLOpt: 0.572 Sensitivity RNAalifold(seed): 0.404 RNASLOpt: 0.521 Positive Predictive Value RNAalifold(seed): 0.923 RNASLOpt: 0.632 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 RNAsubopt vs RNASLOpt Matthews Correlation Coefficient RNAsubopt: 0.615 RNASLOpt: 0.562 Sensitivity RNAsubopt: 0.609 RNASLOpt: 0.521 Positive Predictive Value RNAsubopt: 0.626 RNASLOpt: 0.613 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	875 HotKnots vs RNASLOpt Matthews Correlation Coefficient HotKnots: 0.613 RNASLOpt: 0.562 Sensitivity HotKnots: 0.607 RNASLOpt: 0.520 Positive Predictive Value HotKnots: 0.624 RNASLOpt: 0.613 Number of pairs reference - predicted secondary structure: 875 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 RNAfold vs RNASLOpt Matthews Correlation Coefficient RNAfold: 0.612 RNASLOpt: 0.562 Sensitivity RNAfold: 0.604 RNASLOpt: 0.521 Positive Predictive Value RNAfold: 0.626 RNASLOpt: 0.613 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 RNAshapes vs RNASLOpt Matthews Correlation Coefficient RNAshapes: 0.612 RNASLOpt: 0.562 Sensitivity RNAshapes: 0.602 RNASLOpt: 0.521 Positive Predictive Value RNAshapes: 0.628 RNASLOpt: 0.613 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	86 RNASampler(seed) vs RNASLOpt Matthews Correlation Coefficient RNASampler(seed): 0.557 RNASLOpt: 0.515 Sensitivity RNASampler(seed): 0.389 RNASLOpt: 0.451 Positive Predictive Value RNASampler(seed): 0.802 RNASLOpt: 0.594 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	530 Afold vs RNASLOpt Matthews Correlation Coefficient Afold: 0.558 RNASLOpt: 0.510 Sensitivity Afold: 0.541 RNASLOpt: 0.460 Positive Predictive Value Afold: 0.582 RNASLOpt: 0.572 Number of pairs reference - predicted secondary structure: 530 Wilcoxon single-rank test P-value: 3.56938820447e-08	697 RNASLOpt vs Pknots Matthews Correlation Coefficient RNASLOpt: 0.610 Pknots: 0.606 Sensitivity RNASLOpt: 0.566 Pknots: 0.595 Positive Predictive Value RNASLOpt: 0.665 Pknots: 0.624 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 0.000256148526873	882 McQFold vs RNASLOpt Matthews Correlation Coefficient McQFold: 0.583 RNASLOpt: 0.562 Sensitivity McQFold: 0.557 RNASLOpt: 0.521 Positive Predictive Value McQFold: 0.616 RNASLOpt: 0.613 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 Carnac(20) vs RNASLOpt Matthews Correlation Coefficient Carnac(20): 0.675 RNASLOpt: 0.638 Sensitivity Carnac(20): 0.500 RNASLOpt: 0.594 Positive Predictive Value Carnac(20): 0.915 RNASLOpt: 0.690 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ RNASLOpt vs Cylofold Matthews Correlation Coefficient RNASLOpt: 0.596 Cylofold: 0.577 Sensitivity RNASLOpt: 0.550 Cylofold: 0.554 Positive Predictive Value RNASLOpt: 0.653 Cylofold: 0.608 Number of pairs reference - predicted secondary structure: 796 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs Multilign(seed) Matthews Correlation Coefficient RNASLOpt: 0.544 Multilign(seed): 0.485 Sensitivity RNASLOpt: 0.456 Multilign(seed): 0.386 Positive Predictive Value RNASLOpt: 0.658 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.79203144115e-08	+ RNASLOpt vs RNAwolf Matthews Correlation Coefficient RNASLOpt: 0.562 RNAwolf: 0.518 Sensitivity RNASLOpt: 0.521 RNAwolf: 0.523 Positive Predictive Value RNASLOpt: 0.613 RNAwolf: 0.520 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs PPfold(seed) Matthews Correlation Coefficient RNASLOpt: 0.649 PPfold(seed): 0.380 Sensitivity RNASLOpt: 0.595 PPfold(seed): 0.170 Positive Predictive Value RNASLOpt: 0.714 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs Murlet(seed) Matthews Correlation Coefficient RNASLOpt: 0.546 Murlet(seed): 0.468 Sensitivity RNASLOpt: 0.480 Murlet(seed): 0.266 Positive Predictive Value RNASLOpt: 0.625 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs Alterna Matthews Correlation Coefficient RNASLOpt: 0.612 Alterna: 0.552 Sensitivity RNASLOpt: 0.567 Alterna: 0.547 Positive Predictive Value RNASLOpt: 0.667 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs Carnac(seed) Matthews Correlation Coefficient RNASLOpt: 0.569 Carnac(seed): 0.415 Sensitivity RNASLOpt: 0.511 Carnac(seed): 0.196 Positive Predictive Value RNASLOpt: 0.640 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs Vsfold4 Matthews Correlation Coefficient RNASLOpt: 0.562 Vsfold4: 0.487 Sensitivity RNASLOpt: 0.521 Vsfold4: 0.447 Positive Predictive Value RNASLOpt: 0.613 Vsfold4: 0.537 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs RSpredict(seed) Matthews Correlation Coefficient RNASLOpt: 0.579 RSpredict(seed): 0.373 Sensitivity RNASLOpt: 0.530 RSpredict(seed): 0.251 Positive Predictive Value RNASLOpt: 0.638 RSpredict(seed): 0.562 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs Vsfold5 Matthews Correlation Coefficient RNASLOpt: 0.562 Vsfold5: 0.477 Sensitivity RNASLOpt: 0.521 Vsfold5: 0.450 Positive Predictive Value RNASLOpt: 0.613 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs RDfolder Matthews Correlation Coefficient RNASLOpt: 0.612 RDfolder: 0.520 Sensitivity RNASLOpt: 0.567 RDfolder: 0.464 Positive Predictive Value RNASLOpt: 0.667 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs MCFold Matthews Correlation Coefficient RNASLOpt: 0.577 MCFold: 0.473 Sensitivity RNASLOpt: 0.531 MCFold: 0.524 Positive Predictive Value RNASLOpt: 0.633 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs NanoFolder Matthews Correlation Coefficient RNASLOpt: 0.569 NanoFolder: 0.335 Sensitivity RNASLOpt: 0.520 NanoFolder: 0.384 Positive Predictive Value RNASLOpt: 0.628 NanoFolder: 0.301 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNASLOpt vs Mastr(seed) Matthews Correlation Coefficient RNASLOpt: 0.573 Mastr(seed): 0.263 Sensitivity RNASLOpt: 0.526 Mastr(seed): 0.089 Positive Predictive Value RNASLOpt: 0.629 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08
Cylofold	796 ContextFold vs Cylofold Matthews Correlation Coefficient ContextFold: 0.804 Cylofold: 0.577 Sensitivity ContextFold: 0.764 Cylofold: 0.554 Positive Predictive Value ContextFold: 0.849 Cylofold: 0.608 Number of pairs reference - predicted secondary structure: 796 Wilcoxon single-rank test P-value: 3.56938820447e-08	304 TurboFold(20) vs Cylofold Matthews Correlation Coefficient TurboFold(20): 0.892 Cylofold: 0.557 Sensitivity TurboFold(20): 0.864 Cylofold: 0.543 Positive Predictive Value TurboFold(20): 0.922 Cylofold: 0.577 Number of pairs reference - predicted secondary structure: 304 Wilcoxon single-rank test P-value: 3.56938820447e-08	197 CentroidAlifold(seed) vs Cylofold Matthews Correlation Coefficient CentroidAlifold(seed): 0.785 Cylofold: 0.518 Sensitivity CentroidAlifold(seed): 0.694 Cylofold: 0.491 Positive Predictive Value CentroidAlifold(seed): 0.892 Cylofold: 0.552 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	796 CentroidHomfold‑LAST vs Cylofold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.765 Cylofold: 0.577 Sensitivity CentroidHomfold‑LAST: 0.707 Cylofold: 0.554 Positive Predictive Value CentroidHomfold‑LAST: 0.832 Cylofold: 0.608 Number of pairs reference - predicted secondary structure: 796 Wilcoxon single-rank test P-value: 3.56938820447e-08	464 PETfold_pre2.0(seed) vs Cylofold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.881 Cylofold: 0.580 Sensitivity PETfold_pre2.0(seed): 0.828 Cylofold: 0.568 Positive Predictive Value PETfold_pre2.0(seed): 0.938 Cylofold: 0.598 Number of pairs reference - predicted secondary structure: 464 Wilcoxon single-rank test P-value: 3.56938820447e-08	32 TurboFold(seed) vs Cylofold Matthews Correlation Coefficient TurboFold(seed): 0.800 Cylofold: 0.653 Sensitivity TurboFold(seed): 0.770 Cylofold: 0.626 Positive Predictive Value TurboFold(seed): 0.833 Cylofold: 0.686 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	214 MXScarna(seed) vs Cylofold Matthews Correlation Coefficient MXScarna(seed): 0.760 Cylofold: 0.520 Sensitivity MXScarna(seed): 0.725 Cylofold: 0.495 Positive Predictive Value MXScarna(seed): 0.801 Cylofold: 0.552 Number of pairs reference - predicted secondary structure: 214 Wilcoxon single-rank test P-value: 3.56938820447e-08	304 CentroidAlifold(20) vs Cylofold Matthews Correlation Coefficient CentroidAlifold(20): 0.849 Cylofold: 0.557 Sensitivity CentroidAlifold(20): 0.753 Cylofold: 0.543 Positive Predictive Value CentroidAlifold(20): 0.959 Cylofold: 0.577 Number of pairs reference - predicted secondary structure: 304 Wilcoxon single-rank test P-value: 3.56938820447e-08	304 PETfold_pre2.0(20) vs Cylofold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.845 Cylofold: 0.557 Sensitivity PETfold_pre2.0(20): 0.735 Cylofold: 0.543 Positive Predictive Value PETfold_pre2.0(20): 0.974 Cylofold: 0.577 Number of pairs reference - predicted secondary structure: 304 Wilcoxon single-rank test P-value: 3.56938820447e-08	304 MXScarna(20) vs Cylofold Matthews Correlation Coefficient MXScarna(20): 0.841 Cylofold: 0.557 Sensitivity MXScarna(20): 0.795 Cylofold: 0.543 Positive Predictive Value MXScarna(20): 0.892 Cylofold: 0.577 Number of pairs reference - predicted secondary structure: 304 Wilcoxon single-rank test P-value: 3.56938820447e-08	298 PPfold(20) vs Cylofold Matthews Correlation Coefficient PPfold(20): 0.837 Cylofold: 0.560 Sensitivity PPfold(20): 0.719 Cylofold: 0.546 Positive Predictive Value PPfold(20): 0.976 Cylofold: 0.579 Number of pairs reference - predicted secondary structure: 298 Wilcoxon single-rank test P-value: 3.56938820447e-08	304 RNAalifold(20) vs Cylofold Matthews Correlation Coefficient RNAalifold(20): 0.816 Cylofold: 0.557 Sensitivity RNAalifold(20): 0.690 Cylofold: 0.543 Positive Predictive Value RNAalifold(20): 0.968 Cylofold: 0.577 Number of pairs reference - predicted secondary structure: 304 Wilcoxon single-rank test P-value: 3.56938820447e-08	304 RSpredict(20) vs Cylofold Matthews Correlation Coefficient RSpredict(20): 0.794 Cylofold: 0.557 Sensitivity RSpredict(20): 0.700 Cylofold: 0.543 Positive Predictive Value RSpredict(20): 0.903 Cylofold: 0.577 Number of pairs reference - predicted secondary structure: 304 Wilcoxon single-rank test P-value: 3.56938820447e-08	796 IPknot vs Cylofold Matthews Correlation Coefficient IPknot: 0.719 Cylofold: 0.577 Sensitivity IPknot: 0.687 Cylofold: 0.554 Positive Predictive Value IPknot: 0.757 Cylofold: 0.608 Number of pairs reference - predicted secondary structure: 796 Wilcoxon single-rank test P-value: 3.56938820447e-08	295 Multilign(20) vs Cylofold Matthews Correlation Coefficient Multilign(20): 0.783 Cylofold: 0.563 Sensitivity Multilign(20): 0.695 Cylofold: 0.549 Positive Predictive Value Multilign(20): 0.884 Cylofold: 0.583 Number of pairs reference - predicted secondary structure: 295 Wilcoxon single-rank test P-value: 3.56938820447e-08	796 CentroidFold vs Cylofold Matthews Correlation Coefficient CentroidFold: 0.676 Cylofold: 0.577 Sensitivity CentroidFold: 0.641 Cylofold: 0.554 Positive Predictive Value CentroidFold: 0.718 Cylofold: 0.608 Number of pairs reference - predicted secondary structure: 796 Wilcoxon single-rank test P-value: 3.56938820447e-08	796 Contrafold vs Cylofold Matthews Correlation Coefficient Contrafold: 0.673 Cylofold: 0.577 Sensitivity Contrafold: 0.662 Cylofold: 0.554 Positive Predictive Value Contrafold: 0.689 Cylofold: 0.608 Number of pairs reference - predicted secondary structure: 796 Wilcoxon single-rank test P-value: 3.56938820447e-08	299 RNASampler(20) vs Cylofold Matthews Correlation Coefficient RNASampler(20): 0.773 Cylofold: 0.559 Sensitivity RNASampler(20): 0.625 Cylofold: 0.546 Positive Predictive Value RNASampler(20): 0.959 Cylofold: 0.579 Number of pairs reference - predicted secondary structure: 299 Wilcoxon single-rank test P-value: 3.56938820447e-08	303 Murlet(20) vs Cylofold Matthews Correlation Coefficient Murlet(20): 0.751 Cylofold: 0.558 Sensitivity Murlet(20): 0.620 Cylofold: 0.544 Positive Predictive Value Murlet(20): 0.913 Cylofold: 0.578 Number of pairs reference - predicted secondary structure: 303 Wilcoxon single-rank test P-value: 3.56938820447e-08	67 CMfinder(seed) vs Cylofold Matthews Correlation Coefficient CMfinder(seed): 0.599 Cylofold: 0.465 Sensitivity CMfinder(seed): 0.469 Cylofold: 0.415 Positive Predictive Value CMfinder(seed): 0.772 Cylofold: 0.531 Number of pairs reference - predicted secondary structure: 67 Wilcoxon single-rank test P-value: 3.56938820447e-08	796 MaxExpect vs Cylofold Matthews Correlation Coefficient MaxExpect: 0.660 Cylofold: 0.577 Sensitivity MaxExpect: 0.642 Cylofold: 0.554 Positive Predictive Value MaxExpect: 0.684 Cylofold: 0.608 Number of pairs reference - predicted secondary structure: 796 Wilcoxon single-rank test P-value: 3.56938820447e-08	300 CMfinder(20) vs Cylofold Matthews Correlation Coefficient CMfinder(20): 0.741 Cylofold: 0.559 Sensitivity CMfinder(20): 0.610 Cylofold: 0.546 Positive Predictive Value CMfinder(20): 0.903 Cylofold: 0.578 Number of pairs reference - predicted secondary structure: 300 Wilcoxon single-rank test P-value: 3.56938820447e-08	795 CRWrnafold vs Cylofold Matthews Correlation Coefficient CRWrnafold: 0.667 Cylofold: 0.577 Sensitivity CRWrnafold: 0.651 Cylofold: 0.553 Positive Predictive Value CRWrnafold: 0.688 Cylofold: 0.608 Number of pairs reference - predicted secondary structure: 795 Wilcoxon single-rank test P-value: 3.56938820447e-08	796 ProbKnot vs Cylofold Matthews Correlation Coefficient ProbKnot: 0.658 Cylofold: 0.577 Sensitivity ProbKnot: 0.649 Cylofold: 0.554 Positive Predictive Value ProbKnot: 0.673 Cylofold: 0.608 Number of pairs reference - predicted secondary structure: 796 Wilcoxon single-rank test P-value: 3.56938820447e-08	304 Mastr(20) vs Cylofold Matthews Correlation Coefficient Mastr(20): 0.713 Cylofold: 0.557 Sensitivity Mastr(20): 0.641 Cylofold: 0.543 Positive Predictive Value Mastr(20): 0.796 Cylofold: 0.577 Number of pairs reference - predicted secondary structure: 304 Wilcoxon single-rank test P-value: 3.56938820447e-08	796 Fold vs Cylofold Matthews Correlation Coefficient Fold: 0.654 Cylofold: 0.577 Sensitivity Fold: 0.644 Cylofold: 0.554 Positive Predictive Value Fold: 0.670 Cylofold: 0.608 Number of pairs reference - predicted secondary structure: 796 Wilcoxon single-rank test P-value: 3.56938820447e-08	796 UNAFold vs Cylofold Matthews Correlation Coefficient UNAFold: 0.641 Cylofold: 0.577 Sensitivity UNAFold: 0.625 Cylofold: 0.554 Positive Predictive Value UNAFold: 0.662 Cylofold: 0.608 Number of pairs reference - predicted secondary structure: 796 Wilcoxon single-rank test P-value: 3.56938820447e-08	796 PknotsRG vs Cylofold Matthews Correlation Coefficient PknotsRG: 0.639 Cylofold: 0.577 Sensitivity PknotsRG: 0.630 Cylofold: 0.554 Positive Predictive Value PknotsRG: 0.654 Cylofold: 0.608 Number of pairs reference - predicted secondary structure: 796 Wilcoxon single-rank test P-value: 3.56938820447e-08	796 Sfold vs Cylofold Matthews Correlation Coefficient Sfold: 0.641 Cylofold: 0.577 Sensitivity Sfold: 0.604 Cylofold: 0.554 Positive Predictive Value Sfold: 0.687 Cylofold: 0.608 Number of pairs reference - predicted secondary structure: 796 Wilcoxon single-rank test P-value: 3.56938820447e-08	187 RNAalifold(seed) vs Cylofold Matthews Correlation Coefficient RNAalifold(seed): 0.578 Cylofold: 0.512 Sensitivity RNAalifold(seed): 0.370 Cylofold: 0.484 Positive Predictive Value RNAalifold(seed): 0.909 Cylofold: 0.548 Number of pairs reference - predicted secondary structure: 187 Wilcoxon single-rank test P-value: 3.56938820447e-08	796 RNAsubopt vs Cylofold Matthews Correlation Coefficient RNAsubopt: 0.641 Cylofold: 0.577 Sensitivity RNAsubopt: 0.633 Cylofold: 0.554 Positive Predictive Value RNAsubopt: 0.654 Cylofold: 0.608 Number of pairs reference - predicted secondary structure: 796 Wilcoxon single-rank test P-value: 3.56938820447e-08	796 HotKnots vs Cylofold Matthews Correlation Coefficient HotKnots: 0.638 Cylofold: 0.577 Sensitivity HotKnots: 0.631 Cylofold: 0.554 Positive Predictive Value HotKnots: 0.651 Cylofold: 0.608 Number of pairs reference - predicted secondary structure: 796 Wilcoxon single-rank test P-value: 3.56938820447e-08	796 RNAfold vs Cylofold Matthews Correlation Coefficient RNAfold: 0.636 Cylofold: 0.577 Sensitivity RNAfold: 0.626 Cylofold: 0.554 Positive Predictive Value RNAfold: 0.653 Cylofold: 0.608 Number of pairs reference - predicted secondary structure: 796 Wilcoxon single-rank test P-value: 3.56938820447e-08	796 RNAshapes vs Cylofold Matthews Correlation Coefficient RNAshapes: 0.634 Cylofold: 0.577 Sensitivity RNAshapes: 0.623 Cylofold: 0.554 Positive Predictive Value RNAshapes: 0.651 Cylofold: 0.608 Number of pairs reference - predicted secondary structure: 796 Wilcoxon single-rank test P-value: 3.56938820447e-08	75 RNASampler(seed) vs Cylofold Matthews Correlation Coefficient RNASampler(seed): 0.514 Cylofold: 0.503 Sensitivity RNASampler(seed): 0.335 Cylofold: 0.455 Positive Predictive Value RNASampler(seed): 0.797 Cylofold: 0.565 Number of pairs reference - predicted secondary structure: 75 Wilcoxon single-rank test P-value: 1.80472700427e-05	479 Afold vs Cylofold Matthews Correlation Coefficient Afold: 0.582 Cylofold: 0.544 Sensitivity Afold: 0.563 Cylofold: 0.507 Positive Predictive Value Afold: 0.609 Cylofold: 0.591 Number of pairs reference - predicted secondary structure: 479 Wilcoxon single-rank test P-value: 3.56938820447e-08	676 Cylofold vs Pknots Matthews Correlation Coefficient Cylofold: 0.621 Pknots: 0.614 Sensitivity Cylofold: 0.599 Pknots: 0.603 Positive Predictive Value Cylofold: 0.650 Pknots: 0.632 Number of pairs reference - predicted secondary structure: 676 Wilcoxon single-rank test P-value: 3.85233844192e-08	796 McQFold vs Cylofold Matthews Correlation Coefficient McQFold: 0.617 Cylofold: 0.577 Sensitivity McQFold: 0.587 Cylofold: 0.554 Positive Predictive Value McQFold: 0.654 Cylofold: 0.608 Number of pairs reference - predicted secondary structure: 796 Wilcoxon single-rank test P-value: 3.56938820447e-08	304 Carnac(20) vs Cylofold Matthews Correlation Coefficient Carnac(20): 0.676 Cylofold: 0.557 Sensitivity Carnac(20): 0.499 Cylofold: 0.543 Positive Predictive Value Carnac(20): 0.918 Cylofold: 0.577 Number of pairs reference - predicted secondary structure: 304 Wilcoxon single-rank test P-value: 3.56938820447e-08	796 RNASLOpt vs Cylofold Matthews Correlation Coefficient RNASLOpt: 0.596 Cylofold: 0.577 Sensitivity RNASLOpt: 0.550 Cylofold: 0.554 Positive Predictive Value RNASLOpt: 0.653 Cylofold: 0.608 Number of pairs reference - predicted secondary structure: 796 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ Cylofold vs Multilign(seed) Matthews Correlation Coefficient Cylofold: 0.766 Multilign(seed): 0.475 Sensitivity Cylofold: 0.719 Multilign(seed): 0.372 Positive Predictive Value Cylofold: 0.822 Multilign(seed): 0.617 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 7.06485094932e-09	+ Cylofold vs RNAwolf Matthews Correlation Coefficient Cylofold: 0.577 RNAwolf: 0.545 Sensitivity Cylofold: 0.554 RNAwolf: 0.547 Positive Predictive Value Cylofold: 0.608 RNAwolf: 0.549 Number of pairs reference - predicted secondary structure: 796 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs PPfold(seed) Matthews Correlation Coefficient Cylofold: 0.624 PPfold(seed): 0.375 Sensitivity Cylofold: 0.593 PPfold(seed): 0.167 Positive Predictive Value Cylofold: 0.661 PPfold(seed): 0.845 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs Murlet(seed) Matthews Correlation Coefficient Cylofold: 0.516 Murlet(seed): 0.505 Sensitivity Cylofold: 0.469 Murlet(seed): 0.315 Positive Predictive Value Cylofold: 0.577 Murlet(seed): 0.817 Number of pairs reference - predicted secondary structure: 80 Wilcoxon single-rank test P-value: 9.18042150391e-06	+ Cylofold vs Alterna Matthews Correlation Coefficient Cylofold: 0.621 Alterna: 0.555 Sensitivity Cylofold: 0.599 Alterna: 0.549 Positive Predictive Value Cylofold: 0.650 Alterna: 0.569 Number of pairs reference - predicted secondary structure: 673 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs Carnac(seed) Matthews Correlation Coefficient Cylofold: 0.541 Carnac(seed): 0.408 Sensitivity Cylofold: 0.502 Carnac(seed): 0.189 Positive Predictive Value Cylofold: 0.591 Carnac(seed): 0.888 Number of pairs reference - predicted secondary structure: 112 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs Vsfold4 Matthews Correlation Coefficient Cylofold: 0.577 Vsfold4: 0.515 Sensitivity Cylofold: 0.554 Vsfold4: 0.472 Positive Predictive Value Cylofold: 0.608 Vsfold4: 0.570 Number of pairs reference - predicted secondary structure: 796 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs RSpredict(seed) Matthews Correlation Coefficient Cylofold: 0.518 RSpredict(seed): 0.402 Sensitivity Cylofold: 0.491 RSpredict(seed): 0.279 Positive Predictive Value Cylofold: 0.552 RSpredict(seed): 0.588 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs Vsfold5 Matthews Correlation Coefficient Cylofold: 0.577 Vsfold5: 0.498 Sensitivity Cylofold: 0.554 Vsfold5: 0.469 Positive Predictive Value Cylofold: 0.608 Vsfold5: 0.536 Number of pairs reference - predicted secondary structure: 796 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs RDfolder Matthews Correlation Coefficient Cylofold: 0.621 RDfolder: 0.528 Sensitivity Cylofold: 0.599 RDfolder: 0.470 Positive Predictive Value Cylofold: 0.650 RDfolder: 0.601 Number of pairs reference - predicted secondary structure: 673 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs MCFold Matthews Correlation Coefficient Cylofold: 0.584 MCFold: 0.487 Sensitivity Cylofold: 0.559 MCFold: 0.542 Positive Predictive Value Cylofold: 0.617 MCFold: 0.447 Number of pairs reference - predicted secondary structure: 714 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs NanoFolder Matthews Correlation Coefficient Cylofold: 0.567 NanoFolder: 0.349 Sensitivity Cylofold: 0.536 NanoFolder: 0.400 Positive Predictive Value Cylofold: 0.606 NanoFolder: 0.313 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Cylofold vs Mastr(seed) Matthews Correlation Coefficient Cylofold: 0.520 Mastr(seed): 0.285 Sensitivity Cylofold: 0.495 Mastr(seed): 0.101 Positive Predictive Value Cylofold: 0.553 Mastr(seed): 0.807 Number of pairs reference - predicted secondary structure: 215 Wilcoxon single-rank test P-value: 3.56938820447e-08
Multilign(seed)	13 ContextFold vs Multilign(seed) Matthews Correlation Coefficient ContextFold: 0.568 Multilign(seed): 0.485 Sensitivity ContextFold: 0.512 Multilign(seed): 0.386 Positive Predictive Value ContextFold: 0.640 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.93248927742e-08	3 TurboFold(20) vs Multilign(seed) Matthews Correlation Coefficient TurboFold(20): 0.571 Multilign(seed): 0.334 Sensitivity TurboFold(20): 0.512 Multilign(seed): 0.186 Positive Predictive Value TurboFold(20): 0.647 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	13 CentroidAlifold(seed) vs Multilign(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.683 Multilign(seed): 0.485 Sensitivity CentroidAlifold(seed): 0.516 Multilign(seed): 0.386 Positive Predictive Value CentroidAlifold(seed): 0.910 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.34193807955e-08	13 CentroidHomfold‑LAST vs Multilign(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.597 Multilign(seed): 0.485 Sensitivity CentroidHomfold‑LAST: 0.498 Multilign(seed): 0.386 Positive Predictive Value CentroidHomfold‑LAST: 0.723 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.28439804626e-08	13 PETfold_pre2.0(seed) vs Multilign(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.595 Multilign(seed): 0.485 Sensitivity PETfold_pre2.0(seed): 0.498 Multilign(seed): 0.386 Positive Predictive Value PETfold_pre2.0(seed): 0.718 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.12160100812e-08	13 TurboFold(seed) vs Multilign(seed) Matthews Correlation Coefficient TurboFold(seed): 0.597 Multilign(seed): 0.485 Sensitivity TurboFold(seed): 0.498 Multilign(seed): 0.386 Positive Predictive Value TurboFold(seed): 0.723 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.00627773251e-08	13 MXScarna(seed) vs Multilign(seed) Matthews Correlation Coefficient MXScarna(seed): 0.557 Multilign(seed): 0.485 Sensitivity MXScarna(seed): 0.540 Multilign(seed): 0.386 Positive Predictive Value MXScarna(seed): 0.583 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.54914456376e-08	3 CentroidAlifold(20) vs Multilign(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.693 Multilign(seed): 0.334 Sensitivity CentroidAlifold(20): 0.581 Multilign(seed): 0.186 Positive Predictive Value CentroidAlifold(20): 0.833 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	3 PETfold_pre2.0(20) vs Multilign(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.473 Multilign(seed): 0.334 Sensitivity PETfold_pre2.0(20): 0.326 Multilign(seed): 0.186 Positive Predictive Value PETfold_pre2.0(20): 0.700 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	3 MXScarna(20) vs Multilign(seed) Matthews Correlation Coefficient MXScarna(20): 0.749 Multilign(seed): 0.334 Sensitivity MXScarna(20): 0.698 Multilign(seed): 0.186 Positive Predictive Value MXScarna(20): 0.811 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	3 PPfold(20) vs Multilign(seed) Matthews Correlation Coefficient PPfold(20): 0.531 Multilign(seed): 0.334 Sensitivity PPfold(20): 0.326 Multilign(seed): 0.186 Positive Predictive Value PPfold(20): 0.875 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	3 RNAalifold(20) vs Multilign(seed) Matthews Correlation Coefficient RNAalifold(20): 0.568 Multilign(seed): 0.334 Sensitivity RNAalifold(20): 0.326 Multilign(seed): 0.186 Positive Predictive Value RNAalifold(20): 1.000 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	3 RSpredict(20) vs Multilign(seed) Matthews Correlation Coefficient RSpredict(20): 0.739 Multilign(seed): 0.334 Sensitivity RSpredict(20): 0.698 Multilign(seed): 0.186 Positive Predictive Value RSpredict(20): 0.789 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	13 IPknot vs Multilign(seed) Matthews Correlation Coefficient IPknot: 0.581 Multilign(seed): 0.485 Sensitivity IPknot: 0.502 Multilign(seed): 0.386 Positive Predictive Value IPknot: 0.679 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.16131455263e-08	3 Multilign(20) vs Multilign(seed) Matthews Correlation Coefficient Multilign(20): 0.588 Multilign(seed): 0.334 Sensitivity Multilign(20): 0.349 Multilign(seed): 0.186 Positive Predictive Value Multilign(20): 1.000 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	13 CentroidFold vs Multilign(seed) Matthews Correlation Coefficient CentroidFold: 0.540 Multilign(seed): 0.485 Sensitivity CentroidFold: 0.456 Multilign(seed): 0.386 Positive Predictive Value CentroidFold: 0.649 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.86109605532e-08	13 Contrafold vs Multilign(seed) Matthews Correlation Coefficient Contrafold: 0.525 Multilign(seed): 0.485 Sensitivity Contrafold: 0.460 Multilign(seed): 0.386 Positive Predictive Value Contrafold: 0.607 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.89649746203e-08	3 RNASampler(20) vs Multilign(seed) Matthews Correlation Coefficient RNASampler(20): 0.536 Multilign(seed): 0.334 Sensitivity RNASampler(20): 0.349 Multilign(seed): 0.186 Positive Predictive Value RNASampler(20): 0.833 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	3 Murlet(20) vs Multilign(seed) Matthews Correlation Coefficient Murlet(20): 0.568 Multilign(seed): 0.334 Sensitivity Murlet(20): 0.326 Multilign(seed): 0.186 Positive Predictive Value Murlet(20): 1.000 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	10 CMfinder(seed) vs Multilign(seed) Matthews Correlation Coefficient CMfinder(seed): 0.497 Multilign(seed): 0.444 Sensitivity CMfinder(seed): 0.354 Multilign(seed): 0.335 Positive Predictive Value CMfinder(seed): 0.707 Multilign(seed): 0.598 Number of pairs reference - predicted secondary structure: 10 Wilcoxon single-rank test P-value: 5.70361883708e-09	13 MaxExpect vs Multilign(seed) Matthews Correlation Coefficient MaxExpect: 0.497 Multilign(seed): 0.485 Sensitivity MaxExpect: 0.456 Multilign(seed): 0.386 Positive Predictive Value MaxExpect: 0.551 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.14576075128e-05	3 CMfinder(20) vs Multilign(seed) Matthews Correlation Coefficient CMfinder(20): 0.514 Multilign(seed): 0.334 Sensitivity CMfinder(20): 0.395 Multilign(seed): 0.186 Positive Predictive Value CMfinder(20): 0.680 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	13 Multilign(seed) vs CRWrnafold Matthews Correlation Coefficient Multilign(seed): 0.485 CRWrnafold: 0.415 Sensitivity Multilign(seed): 0.386 CRWrnafold: 0.395 Positive Predictive Value Multilign(seed): 0.619 CRWrnafold: 0.447 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.04409141234e-08	13 ProbKnot vs Multilign(seed) Matthews Correlation Coefficient ProbKnot: 0.505 Multilign(seed): 0.485 Sensitivity ProbKnot: 0.479 Multilign(seed): 0.386 Positive Predictive Value ProbKnot: 0.542 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.23248012054e-07	3 Mastr(20) vs Multilign(seed) Matthews Correlation Coefficient Mastr(20): 0.775 Multilign(seed): 0.334 Sensitivity Mastr(20): 0.721 Multilign(seed): 0.186 Positive Predictive Value Mastr(20): 0.838 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	13 Multilign(seed) vs Fold Matthews Correlation Coefficient Multilign(seed): 0.485 Fold: 0.430 Sensitivity Multilign(seed): 0.386 Fold: 0.405 Positive Predictive Value Multilign(seed): 0.619 Fold: 0.468 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.82627677697e-08	13 Multilign(seed) vs UNAFold Matthews Correlation Coefficient Multilign(seed): 0.485 UNAFold: 0.469 Sensitivity Multilign(seed): 0.386 UNAFold: 0.437 Positive Predictive Value Multilign(seed): 0.619 UNAFold: 0.514 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 5.59774301112e-05	13 PknotsRG vs Multilign(seed) Matthews Correlation Coefficient PknotsRG: 0.742 Multilign(seed): 0.485 Sensitivity PknotsRG: 0.716 Multilign(seed): 0.386 Positive Predictive Value PknotsRG: 0.774 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.57237423209e-08	13 Multilign(seed) vs Sfold Matthews Correlation Coefficient Multilign(seed): 0.485 Sfold: 0.456 Sensitivity Multilign(seed): 0.386 Sfold: 0.414 Positive Predictive Value Multilign(seed): 0.619 Sfold: 0.511 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 8.95709882289e-08	13 RNAalifold(seed) vs Multilign(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.590 Multilign(seed): 0.485 Sensitivity RNAalifold(seed): 0.447 Multilign(seed): 0.386 Positive Predictive Value RNAalifold(seed): 0.787 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.45096400029e-08	13 Multilign(seed) vs RNAsubopt Matthews Correlation Coefficient Multilign(seed): 0.485 RNAsubopt: 0.465 Sensitivity Multilign(seed): 0.386 RNAsubopt: 0.437 Positive Predictive Value Multilign(seed): 0.619 RNAsubopt: 0.505 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 9.94451398341e-06	13 HotKnots vs Multilign(seed) Matthews Correlation Coefficient HotKnots: 0.519 Multilign(seed): 0.485 Sensitivity HotKnots: 0.521 Multilign(seed): 0.386 Positive Predictive Value HotKnots: 0.526 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 4.52862048029e-08	13 Multilign(seed) vs RNAfold Matthews Correlation Coefficient Multilign(seed): 0.485 RNAfold: 0.462 Sensitivity Multilign(seed): 0.386 RNAfold: 0.437 Positive Predictive Value Multilign(seed): 0.619 RNAfold: 0.497 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 3.25008686899e-05	13 Multilign(seed) vs RNAshapes Matthews Correlation Coefficient Multilign(seed): 0.485 RNAshapes: 0.468 Sensitivity Multilign(seed): 0.386 RNAshapes: 0.437 Positive Predictive Value Multilign(seed): 0.619 RNAshapes: 0.511 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.66432434427e-06	13 RNASampler(seed) vs Multilign(seed) Matthews Correlation Coefficient RNASampler(seed): 0.497 Multilign(seed): 0.485 Sensitivity RNASampler(seed): 0.381 Multilign(seed): 0.386 Positive Predictive Value RNASampler(seed): 0.656 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 5.14700275415e-08	12 Afold vs Multilign(seed) Matthews Correlation Coefficient Afold: 0.482 Multilign(seed): 0.473 Sensitivity Afold: 0.447 Multilign(seed): 0.371 Positive Predictive Value Afold: 0.530 Multilign(seed): 0.613 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 0.00176601553263	13 Pknots vs Multilign(seed) Matthews Correlation Coefficient Pknots: 0.699 Multilign(seed): 0.485 Sensitivity Pknots: 0.684 Multilign(seed): 0.386 Positive Predictive Value Pknots: 0.721 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.74172190343e-08	13 McQFold vs Multilign(seed) Matthews Correlation Coefficient McQFold: 0.765 Multilign(seed): 0.485 Sensitivity McQFold: 0.730 Multilign(seed): 0.386 Positive Predictive Value McQFold: 0.805 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.24270395587e-08	3 Carnac(20) vs Multilign(seed) Matthews Correlation Coefficient Carnac(20): 0.588 Multilign(seed): 0.334 Sensitivity Carnac(20): 0.349 Multilign(seed): 0.186 Positive Predictive Value Carnac(20): 1.000 Multilign(seed): 0.615 Number of pairs reference - predicted secondary structure: 3 Wilcoxon single-rank test P-value: 0.0	13 RNASLOpt vs Multilign(seed) Matthews Correlation Coefficient RNASLOpt: 0.544 Multilign(seed): 0.485 Sensitivity RNASLOpt: 0.456 Multilign(seed): 0.386 Positive Predictive Value RNASLOpt: 0.658 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.79203144115e-08	12 Cylofold vs Multilign(seed) Matthews Correlation Coefficient Cylofold: 0.766 Multilign(seed): 0.475 Sensitivity Cylofold: 0.719 Multilign(seed): 0.372 Positive Predictive Value Cylofold: 0.822 Multilign(seed): 0.617 Number of pairs reference - predicted secondary structure: 12 Wilcoxon single-rank test P-value: 7.06485094932e-09		+ Multilign(seed) vs RNAwolf Matthews Correlation Coefficient Multilign(seed): 0.485 RNAwolf: 0.380 Sensitivity Multilign(seed): 0.386 RNAwolf: 0.367 Positive Predictive Value Multilign(seed): 0.619 RNAwolf: 0.405 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.38194587311e-08	- PPfold(seed) vs Multilign(seed) Matthews Correlation Coefficient PPfold(seed): 0.614 Multilign(seed): 0.485 Sensitivity PPfold(seed): 0.460 Multilign(seed): 0.386 Positive Predictive Value PPfold(seed): 0.825 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.06323189071e-08	+ Multilign(seed) vs Murlet(seed) Matthews Correlation Coefficient Multilign(seed): 0.485 Murlet(seed): 0.448 Sensitivity Multilign(seed): 0.386 Murlet(seed): 0.284 Positive Predictive Value Multilign(seed): 0.619 Murlet(seed): 0.718 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.96907987703e-08	+ Multilign(seed) vs Alterna Matthews Correlation Coefficient Multilign(seed): 0.485 Alterna: 0.420 Sensitivity Multilign(seed): 0.386 Alterna: 0.391 Positive Predictive Value Multilign(seed): 0.619 Alterna: 0.462 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.36983135185e-08	- Carnac(seed) vs Multilign(seed) Matthews Correlation Coefficient Carnac(seed): 0.566 Multilign(seed): 0.485 Sensitivity Carnac(seed): 0.349 Multilign(seed): 0.386 Positive Predictive Value Carnac(seed): 0.926 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.93248927742e-08	+ Multilign(seed) vs Vsfold4 Matthews Correlation Coefficient Multilign(seed): 0.485 Vsfold4: 0.332 Sensitivity Multilign(seed): 0.386 Vsfold4: 0.298 Positive Predictive Value Multilign(seed): 0.619 Vsfold4: 0.383 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.4651262096e-08	= Multilign(seed) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(seed): 0.485 RSpredict(seed): 0.479 Sensitivity Multilign(seed): 0.386 RSpredict(seed): 0.423 Positive Predictive Value Multilign(seed): 0.619 RSpredict(seed): 0.552 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 0.0114155930811	+ Multilign(seed) vs Vsfold5 Matthews Correlation Coefficient Multilign(seed): 0.485 Vsfold5: 0.418 Sensitivity Multilign(seed): 0.386 Vsfold5: 0.386 Positive Predictive Value Multilign(seed): 0.619 Vsfold5: 0.464 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.93248927742e-08	= Multilign(seed) vs RDfolder Matthews Correlation Coefficient Multilign(seed): 0.485 RDfolder: 0.480 Sensitivity Multilign(seed): 0.386 RDfolder: 0.391 Positive Predictive Value Multilign(seed): 0.619 RDfolder: 0.600 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 0.0656750159858	+ Multilign(seed) vs MCFold Matthews Correlation Coefficient Multilign(seed): 0.485 MCFold: 0.359 Sensitivity Multilign(seed): 0.386 MCFold: 0.419 Positive Predictive Value Multilign(seed): 0.619 MCFold: 0.319 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.06323189071e-08	? NanoFolder vs Multilign(seed) Matthews Correlation Coefficient NanoFolder: 0.560 Multilign(seed): 0.551 Sensitivity NanoFolder: 0.605 Multilign(seed): 0.457 Positive Predictive Value NanoFolder: 0.527 Multilign(seed): 0.673 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	- Mastr(seed) vs Multilign(seed) Matthews Correlation Coefficient Mastr(seed): 0.503 Multilign(seed): 0.485 Sensitivity Mastr(seed): 0.372 Multilign(seed): 0.386 Positive Predictive Value Mastr(seed): 0.690 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 4.84476306662e-07
RNAwolf	882 ContextFold vs RNAwolf Matthews Correlation Coefficient ContextFold: 0.779 RNAwolf: 0.518 Sensitivity ContextFold: 0.741 RNAwolf: 0.523 Positive Predictive Value ContextFold: 0.823 RNAwolf: 0.520 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 TurboFold(20) vs RNAwolf Matthews Correlation Coefficient TurboFold(20): 0.889 RNAwolf: 0.561 Sensitivity TurboFold(20): 0.861 RNAwolf: 0.565 Positive Predictive Value TurboFold(20): 0.919 RNAwolf: 0.561 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	216 CentroidAlifold(seed) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(seed): 0.790 RNAwolf: 0.529 Sensitivity CentroidAlifold(seed): 0.699 RNAwolf: 0.534 Positive Predictive Value CentroidAlifold(seed): 0.896 RNAwolf: 0.529 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 CentroidHomfold‑LAST vs RNAwolf Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.736 RNAwolf: 0.518 Sensitivity CentroidHomfold‑LAST: 0.665 RNAwolf: 0.523 Positive Predictive Value CentroidHomfold‑LAST: 0.818 RNAwolf: 0.520 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	498 PETfold_pre2.0(seed) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.879 RNAwolf: 0.535 Sensitivity PETfold_pre2.0(seed): 0.825 RNAwolf: 0.545 Positive Predictive Value PETfold_pre2.0(seed): 0.938 RNAwolf: 0.532 Number of pairs reference - predicted secondary structure: 498 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 TurboFold(seed) vs RNAwolf Matthews Correlation Coefficient TurboFold(seed): 0.798 RNAwolf: 0.532 Sensitivity TurboFold(seed): 0.766 RNAwolf: 0.527 Positive Predictive Value TurboFold(seed): 0.835 RNAwolf: 0.543 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	233 MXScarna(seed) vs RNAwolf Matthews Correlation Coefficient MXScarna(seed): 0.750 RNAwolf: 0.522 Sensitivity MXScarna(seed): 0.712 RNAwolf: 0.528 Positive Predictive Value MXScarna(seed): 0.793 RNAwolf: 0.522 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 CentroidAlifold(20) vs RNAwolf Matthews Correlation Coefficient CentroidAlifold(20): 0.849 RNAwolf: 0.561 Sensitivity CentroidAlifold(20): 0.754 RNAwolf: 0.565 Positive Predictive Value CentroidAlifold(20): 0.957 RNAwolf: 0.561 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 PETfold_pre2.0(20) vs RNAwolf Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 RNAwolf: 0.561 Sensitivity PETfold_pre2.0(20): 0.737 RNAwolf: 0.565 Positive Predictive Value PETfold_pre2.0(20): 0.975 RNAwolf: 0.561 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 MXScarna(20) vs RNAwolf Matthews Correlation Coefficient MXScarna(20): 0.838 RNAwolf: 0.561 Sensitivity MXScarna(20): 0.791 RNAwolf: 0.565 Positive Predictive Value MXScarna(20): 0.891 RNAwolf: 0.561 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	314 PPfold(20) vs RNAwolf Matthews Correlation Coefficient PPfold(20): 0.839 RNAwolf: 0.560 Sensitivity PPfold(20): 0.721 RNAwolf: 0.565 Positive Predictive Value PPfold(20): 0.977 RNAwolf: 0.561 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RNAalifold(20) vs RNAwolf Matthews Correlation Coefficient RNAalifold(20): 0.816 RNAwolf: 0.561 Sensitivity RNAalifold(20): 0.690 RNAwolf: 0.565 Positive Predictive Value RNAalifold(20): 0.966 RNAwolf: 0.561 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RSpredict(20) vs RNAwolf Matthews Correlation Coefficient RSpredict(20): 0.789 RNAwolf: 0.561 Sensitivity RSpredict(20): 0.693 RNAwolf: 0.565 Positive Predictive Value RSpredict(20): 0.901 RNAwolf: 0.561 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 IPknot vs RNAwolf Matthews Correlation Coefficient IPknot: 0.694 RNAwolf: 0.518 Sensitivity IPknot: 0.661 RNAwolf: 0.523 Positive Predictive Value IPknot: 0.733 RNAwolf: 0.520 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	311 Multilign(20) vs RNAwolf Matthews Correlation Coefficient Multilign(20): 0.784 RNAwolf: 0.560 Sensitivity Multilign(20): 0.697 RNAwolf: 0.565 Positive Predictive Value Multilign(20): 0.885 RNAwolf: 0.560 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 CentroidFold vs RNAwolf Matthews Correlation Coefficient CentroidFold: 0.645 RNAwolf: 0.518 Sensitivity CentroidFold: 0.612 RNAwolf: 0.523 Positive Predictive Value CentroidFold: 0.684 RNAwolf: 0.520 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 Contrafold vs RNAwolf Matthews Correlation Coefficient Contrafold: 0.643 RNAwolf: 0.518 Sensitivity Contrafold: 0.634 RNAwolf: 0.523 Positive Predictive Value Contrafold: 0.657 RNAwolf: 0.520 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	315 RNASampler(20) vs RNAwolf Matthews Correlation Coefficient RNASampler(20): 0.770 RNAwolf: 0.560 Sensitivity RNASampler(20): 0.622 RNAwolf: 0.565 Positive Predictive Value RNASampler(20): 0.957 RNAwolf: 0.561 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	319 Murlet(20) vs RNAwolf Matthews Correlation Coefficient Murlet(20): 0.750 RNAwolf: 0.560 Sensitivity Murlet(20): 0.619 RNAwolf: 0.565 Positive Predictive Value Murlet(20): 0.913 RNAwolf: 0.561 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 CMfinder(seed) vs RNAwolf Matthews Correlation Coefficient CMfinder(seed): 0.571 RNAwolf: 0.369 Sensitivity CMfinder(seed): 0.439 RNAwolf: 0.369 Positive Predictive Value CMfinder(seed): 0.747 RNAwolf: 0.377 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 MaxExpect vs RNAwolf Matthews Correlation Coefficient MaxExpect: 0.633 RNAwolf: 0.518 Sensitivity MaxExpect: 0.617 RNAwolf: 0.523 Positive Predictive Value MaxExpect: 0.654 RNAwolf: 0.520 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	316 CMfinder(20) vs RNAwolf Matthews Correlation Coefficient CMfinder(20): 0.735 RNAwolf: 0.563 Sensitivity CMfinder(20): 0.603 RNAwolf: 0.568 Positive Predictive Value CMfinder(20): 0.899 RNAwolf: 0.563 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	881 CRWrnafold vs RNAwolf Matthews Correlation Coefficient CRWrnafold: 0.630 RNAwolf: 0.518 Sensitivity CRWrnafold: 0.618 RNAwolf: 0.523 Positive Predictive Value CRWrnafold: 0.648 RNAwolf: 0.520 Number of pairs reference - predicted secondary structure: 881 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 ProbKnot vs RNAwolf Matthews Correlation Coefficient ProbKnot: 0.630 RNAwolf: 0.518 Sensitivity ProbKnot: 0.622 RNAwolf: 0.523 Positive Predictive Value ProbKnot: 0.644 RNAwolf: 0.520 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 Mastr(20) vs RNAwolf Matthews Correlation Coefficient Mastr(20): 0.708 RNAwolf: 0.561 Sensitivity Mastr(20): 0.635 RNAwolf: 0.565 Positive Predictive Value Mastr(20): 0.793 RNAwolf: 0.561 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 Fold vs RNAwolf Matthews Correlation Coefficient Fold: 0.628 RNAwolf: 0.518 Sensitivity Fold: 0.620 RNAwolf: 0.523 Positive Predictive Value Fold: 0.641 RNAwolf: 0.520 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 UNAFold vs RNAwolf Matthews Correlation Coefficient UNAFold: 0.620 RNAwolf: 0.518 Sensitivity UNAFold: 0.605 RNAwolf: 0.523 Positive Predictive Value UNAFold: 0.639 RNAwolf: 0.520 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 PknotsRG vs RNAwolf Matthews Correlation Coefficient PknotsRG: 0.617 RNAwolf: 0.518 Sensitivity PknotsRG: 0.610 RNAwolf: 0.523 Positive Predictive Value PknotsRG: 0.630 RNAwolf: 0.520 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 Sfold vs RNAwolf Matthews Correlation Coefficient Sfold: 0.618 RNAwolf: 0.518 Sensitivity Sfold: 0.581 RNAwolf: 0.523 Positive Predictive Value Sfold: 0.663 RNAwolf: 0.520 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	205 RNAalifold(seed) vs RNAwolf Matthews Correlation Coefficient RNAalifold(seed): 0.610 RNAwolf: 0.529 Sensitivity RNAalifold(seed): 0.404 RNAwolf: 0.534 Positive Predictive Value RNAalifold(seed): 0.923 RNAwolf: 0.531 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 RNAsubopt vs RNAwolf Matthews Correlation Coefficient RNAsubopt: 0.615 RNAwolf: 0.518 Sensitivity RNAsubopt: 0.609 RNAwolf: 0.523 Positive Predictive Value RNAsubopt: 0.626 RNAwolf: 0.520 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	875 HotKnots vs RNAwolf Matthews Correlation Coefficient HotKnots: 0.613 RNAwolf: 0.518 Sensitivity HotKnots: 0.607 RNAwolf: 0.523 Positive Predictive Value HotKnots: 0.624 RNAwolf: 0.520 Number of pairs reference - predicted secondary structure: 875 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 RNAfold vs RNAwolf Matthews Correlation Coefficient RNAfold: 0.612 RNAwolf: 0.518 Sensitivity RNAfold: 0.604 RNAwolf: 0.523 Positive Predictive Value RNAfold: 0.626 RNAwolf: 0.520 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 RNAshapes vs RNAwolf Matthews Correlation Coefficient RNAshapes: 0.612 RNAwolf: 0.518 Sensitivity RNAshapes: 0.602 RNAwolf: 0.523 Positive Predictive Value RNAshapes: 0.628 RNAwolf: 0.520 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	86 RNASampler(seed) vs RNAwolf Matthews Correlation Coefficient RNASampler(seed): 0.557 RNAwolf: 0.383 Sensitivity RNASampler(seed): 0.389 RNAwolf: 0.383 Positive Predictive Value RNASampler(seed): 0.802 RNAwolf: 0.391 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	530 Afold vs RNAwolf Matthews Correlation Coefficient Afold: 0.558 RNAwolf: 0.509 Sensitivity Afold: 0.541 RNAwolf: 0.507 Positive Predictive Value Afold: 0.582 RNAwolf: 0.518 Number of pairs reference - predicted secondary structure: 530 Wilcoxon single-rank test P-value: 3.56938820447e-08	697 Pknots vs RNAwolf Matthews Correlation Coefficient Pknots: 0.606 RNAwolf: 0.550 Sensitivity Pknots: 0.595 RNAwolf: 0.554 Positive Predictive Value Pknots: 0.624 RNAwolf: 0.554 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 McQFold vs RNAwolf Matthews Correlation Coefficient McQFold: 0.583 RNAwolf: 0.518 Sensitivity McQFold: 0.557 RNAwolf: 0.523 Positive Predictive Value McQFold: 0.616 RNAwolf: 0.520 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 Carnac(20) vs RNAwolf Matthews Correlation Coefficient Carnac(20): 0.675 RNAwolf: 0.561 Sensitivity Carnac(20): 0.500 RNAwolf: 0.565 Positive Predictive Value Carnac(20): 0.915 RNAwolf: 0.561 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 RNASLOpt vs RNAwolf Matthews Correlation Coefficient RNASLOpt: 0.562 RNAwolf: 0.518 Sensitivity RNASLOpt: 0.521 RNAwolf: 0.523 Positive Predictive Value RNASLOpt: 0.613 RNAwolf: 0.520 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	796 Cylofold vs RNAwolf Matthews Correlation Coefficient Cylofold: 0.577 RNAwolf: 0.545 Sensitivity Cylofold: 0.554 RNAwolf: 0.547 Positive Predictive Value Cylofold: 0.608 RNAwolf: 0.549 Number of pairs reference - predicted secondary structure: 796 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Multilign(seed) vs RNAwolf Matthews Correlation Coefficient Multilign(seed): 0.485 RNAwolf: 0.380 Sensitivity Multilign(seed): 0.386 RNAwolf: 0.367 Positive Predictive Value Multilign(seed): 0.619 RNAwolf: 0.405 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.38194587311e-08		+ RNAwolf vs PPfold(seed) Matthews Correlation Coefficient RNAwolf: 0.615 PPfold(seed): 0.380 Sensitivity RNAwolf: 0.619 PPfold(seed): 0.170 Positive Predictive Value RNAwolf: 0.617 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Murlet(seed) vs RNAwolf Matthews Correlation Coefficient Murlet(seed): 0.468 RNAwolf: 0.407 Sensitivity Murlet(seed): 0.266 RNAwolf: 0.405 Positive Predictive Value Murlet(seed): 0.828 RNAwolf: 0.415 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	= Alterna vs RNAwolf Matthews Correlation Coefficient Alterna: 0.552 RNAwolf: 0.551 Sensitivity Alterna: 0.547 RNAwolf: 0.555 Positive Predictive Value Alterna: 0.566 RNAwolf: 0.555 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 0.808824058118	+ RNAwolf vs Carnac(seed) Matthews Correlation Coefficient RNAwolf: 0.472 Carnac(seed): 0.415 Sensitivity RNAwolf: 0.473 Carnac(seed): 0.196 Positive Predictive Value RNAwolf: 0.478 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAwolf vs Vsfold4 Matthews Correlation Coefficient RNAwolf: 0.518 Vsfold4: 0.487 Sensitivity RNAwolf: 0.523 Vsfold4: 0.447 Positive Predictive Value RNAwolf: 0.520 Vsfold4: 0.537 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAwolf vs RSpredict(seed) Matthews Correlation Coefficient RNAwolf: 0.529 RSpredict(seed): 0.373 Sensitivity RNAwolf: 0.534 RSpredict(seed): 0.251 Positive Predictive Value RNAwolf: 0.529 RSpredict(seed): 0.562 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAwolf vs Vsfold5 Matthews Correlation Coefficient RNAwolf: 0.518 Vsfold5: 0.477 Sensitivity RNAwolf: 0.523 Vsfold5: 0.450 Positive Predictive Value RNAwolf: 0.520 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAwolf vs RDfolder Matthews Correlation Coefficient RNAwolf: 0.551 RDfolder: 0.520 Sensitivity RNAwolf: 0.555 RDfolder: 0.464 Positive Predictive Value RNAwolf: 0.555 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAwolf vs MCFold Matthews Correlation Coefficient RNAwolf: 0.530 MCFold: 0.473 Sensitivity RNAwolf: 0.532 MCFold: 0.524 Positive Predictive Value RNAwolf: 0.534 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAwolf vs NanoFolder Matthews Correlation Coefficient RNAwolf: 0.583 NanoFolder: 0.335 Sensitivity RNAwolf: 0.580 NanoFolder: 0.384 Positive Predictive Value RNAwolf: 0.593 NanoFolder: 0.301 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RNAwolf vs Mastr(seed) Matthews Correlation Coefficient RNAwolf: 0.522 Mastr(seed): 0.263 Sensitivity RNAwolf: 0.528 Mastr(seed): 0.089 Positive Predictive Value RNAwolf: 0.522 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08
PPfold(seed)	40 ContextFold vs PPfold(seed) Matthews Correlation Coefficient ContextFold: 0.868 PPfold(seed): 0.380 Sensitivity ContextFold: 0.845 PPfold(seed): 0.170 Positive Predictive Value ContextFold: 0.894 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 TurboFold(20) vs PPfold(seed) Matthews Correlation Coefficient TurboFold(20): 0.871 PPfold(seed): 0.344 Sensitivity TurboFold(20): 0.870 PPfold(seed): 0.128 Positive Predictive Value TurboFold(20): 0.873 PPfold(seed): 0.927 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.02343278931e-08	40 CentroidAlifold(seed) vs PPfold(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.740 PPfold(seed): 0.380 Sensitivity CentroidAlifold(seed): 0.602 PPfold(seed): 0.170 Positive Predictive Value CentroidAlifold(seed): 0.912 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	40 CentroidHomfold‑LAST vs PPfold(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.794 PPfold(seed): 0.380 Sensitivity CentroidHomfold‑LAST: 0.742 PPfold(seed): 0.170 Positive Predictive Value CentroidHomfold‑LAST: 0.853 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	39 PETfold_pre2.0(seed) vs PPfold(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.765 PPfold(seed): 0.386 Sensitivity PETfold_pre2.0(seed): 0.665 PPfold(seed): 0.176 Positive Predictive Value PETfold_pre2.0(seed): 0.883 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 39 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 TurboFold(seed) vs PPfold(seed) Matthews Correlation Coefficient TurboFold(seed): 0.778 PPfold(seed): 0.524 Sensitivity TurboFold(seed): 0.727 PPfold(seed): 0.325 Positive Predictive Value TurboFold(seed): 0.837 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 4.50425137787e-08	40 MXScarna(seed) vs PPfold(seed) Matthews Correlation Coefficient MXScarna(seed): 0.762 PPfold(seed): 0.380 Sensitivity MXScarna(seed): 0.736 PPfold(seed): 0.170 Positive Predictive Value MXScarna(seed): 0.794 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 CentroidAlifold(20) vs PPfold(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.702 PPfold(seed): 0.344 Sensitivity CentroidAlifold(20): 0.525 PPfold(seed): 0.128 Positive Predictive Value CentroidAlifold(20): 0.942 PPfold(seed): 0.927 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 4.98172311752e-08	23 PETfold_pre2.0(20) vs PPfold(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.616 PPfold(seed): 0.344 Sensitivity PETfold_pre2.0(20): 0.400 PPfold(seed): 0.128 Positive Predictive Value PETfold_pre2.0(20): 0.952 PPfold(seed): 0.927 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.19332990918e-08	23 MXScarna(20) vs PPfold(seed) Matthews Correlation Coefficient MXScarna(20): 0.831 PPfold(seed): 0.344 Sensitivity MXScarna(20): 0.764 PPfold(seed): 0.128 Positive Predictive Value MXScarna(20): 0.906 PPfold(seed): 0.927 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	23 PPfold(20) vs PPfold(seed) Matthews Correlation Coefficient PPfold(20): 0.588 PPfold(seed): 0.344 Sensitivity PPfold(20): 0.365 PPfold(seed): 0.128 Positive Predictive Value PPfold(20): 0.952 PPfold(seed): 0.927 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	23 RNAalifold(20) vs PPfold(seed) Matthews Correlation Coefficient RNAalifold(20): 0.667 PPfold(seed): 0.344 Sensitivity RNAalifold(20): 0.471 PPfold(seed): 0.128 Positive Predictive Value RNAalifold(20): 0.949 PPfold(seed): 0.927 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.1503931209e-08	23 RSpredict(20) vs PPfold(seed) Matthews Correlation Coefficient RSpredict(20): 0.782 PPfold(seed): 0.344 Sensitivity RSpredict(20): 0.666 PPfold(seed): 0.128 Positive Predictive Value RSpredict(20): 0.923 PPfold(seed): 0.927 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 4.98172311752e-08	40 IPknot vs PPfold(seed) Matthews Correlation Coefficient IPknot: 0.802 PPfold(seed): 0.380 Sensitivity IPknot: 0.780 PPfold(seed): 0.170 Positive Predictive Value IPknot: 0.827 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	22 Multilign(20) vs PPfold(seed) Matthews Correlation Coefficient Multilign(20): 0.611 PPfold(seed): 0.354 Sensitivity Multilign(20): 0.462 PPfold(seed): 0.136 Positive Predictive Value Multilign(20): 0.811 PPfold(seed): 0.927 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.19332990918e-08	40 CentroidFold vs PPfold(seed) Matthews Correlation Coefficient CentroidFold: 0.729 PPfold(seed): 0.380 Sensitivity CentroidFold: 0.696 PPfold(seed): 0.170 Positive Predictive Value CentroidFold: 0.767 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	40 Contrafold vs PPfold(seed) Matthews Correlation Coefficient Contrafold: 0.722 PPfold(seed): 0.380 Sensitivity Contrafold: 0.706 PPfold(seed): 0.170 Positive Predictive Value Contrafold: 0.743 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 RNASampler(20) vs PPfold(seed) Matthews Correlation Coefficient RNASampler(20): 0.589 PPfold(seed): 0.344 Sensitivity RNASampler(20): 0.363 PPfold(seed): 0.128 Positive Predictive Value RNASampler(20): 0.960 PPfold(seed): 0.927 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.10776592382e-08	22 Murlet(20) vs PPfold(seed) Matthews Correlation Coefficient Murlet(20): 0.618 PPfold(seed): 0.352 Sensitivity Murlet(20): 0.412 PPfold(seed): 0.135 Positive Predictive Value Murlet(20): 0.932 PPfold(seed): 0.927 Number of pairs reference - predicted secondary structure: 22 Wilcoxon single-rank test P-value: 5.1503931209e-08	13 PPfold(seed) vs CMfinder(seed) Matthews Correlation Coefficient PPfold(seed): 0.600 CMfinder(seed): 0.585 Sensitivity PPfold(seed): 0.455 CMfinder(seed): 0.440 Positive Predictive Value PPfold(seed): 0.798 CMfinder(seed): 0.786 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.60044567142e-05	40 MaxExpect vs PPfold(seed) Matthews Correlation Coefficient MaxExpect: 0.736 PPfold(seed): 0.380 Sensitivity MaxExpect: 0.730 PPfold(seed): 0.170 Positive Predictive Value MaxExpect: 0.746 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 CMfinder(20) vs PPfold(seed) Matthews Correlation Coefficient CMfinder(20): 0.740 PPfold(seed): 0.344 Sensitivity CMfinder(20): 0.595 PPfold(seed): 0.128 Positive Predictive Value CMfinder(20): 0.924 PPfold(seed): 0.927 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 4.94031556815e-08	40 CRWrnafold vs PPfold(seed) Matthews Correlation Coefficient CRWrnafold: 0.702 PPfold(seed): 0.380 Sensitivity CRWrnafold: 0.702 PPfold(seed): 0.170 Positive Predictive Value CRWrnafold: 0.706 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	40 ProbKnot vs PPfold(seed) Matthews Correlation Coefficient ProbKnot: 0.726 PPfold(seed): 0.380 Sensitivity ProbKnot: 0.722 PPfold(seed): 0.170 Positive Predictive Value ProbKnot: 0.733 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 Mastr(20) vs PPfold(seed) Matthews Correlation Coefficient Mastr(20): 0.719 PPfold(seed): 0.344 Sensitivity Mastr(20): 0.576 PPfold(seed): 0.128 Positive Predictive Value Mastr(20): 0.902 PPfold(seed): 0.927 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 5.1503931209e-08	40 Fold vs PPfold(seed) Matthews Correlation Coefficient Fold: 0.737 PPfold(seed): 0.380 Sensitivity Fold: 0.737 PPfold(seed): 0.170 Positive Predictive Value Fold: 0.741 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	40 UNAFold vs PPfold(seed) Matthews Correlation Coefficient UNAFold: 0.688 PPfold(seed): 0.380 Sensitivity UNAFold: 0.685 PPfold(seed): 0.170 Positive Predictive Value UNAFold: 0.696 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	40 PknotsRG vs PPfold(seed) Matthews Correlation Coefficient PknotsRG: 0.752 PPfold(seed): 0.380 Sensitivity PknotsRG: 0.756 PPfold(seed): 0.170 Positive Predictive Value PknotsRG: 0.751 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	40 Sfold vs PPfold(seed) Matthews Correlation Coefficient Sfold: 0.709 PPfold(seed): 0.380 Sensitivity Sfold: 0.686 PPfold(seed): 0.170 Positive Predictive Value Sfold: 0.736 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	31 RNAalifold(seed) vs PPfold(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.588 PPfold(seed): 0.425 Sensitivity RNAalifold(seed): 0.386 PPfold(seed): 0.213 Positive Predictive Value RNAalifold(seed): 0.901 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 31 Wilcoxon single-rank test P-value: 3.56938820447e-08	40 RNAsubopt vs PPfold(seed) Matthews Correlation Coefficient RNAsubopt: 0.721 PPfold(seed): 0.380 Sensitivity RNAsubopt: 0.720 PPfold(seed): 0.170 Positive Predictive Value RNAsubopt: 0.727 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	40 HotKnots vs PPfold(seed) Matthews Correlation Coefficient HotKnots: 0.702 PPfold(seed): 0.380 Sensitivity HotKnots: 0.713 PPfold(seed): 0.170 Positive Predictive Value HotKnots: 0.697 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	40 RNAfold vs PPfold(seed) Matthews Correlation Coefficient RNAfold: 0.701 PPfold(seed): 0.380 Sensitivity RNAfold: 0.702 PPfold(seed): 0.170 Positive Predictive Value RNAfold: 0.705 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	40 RNAshapes vs PPfold(seed) Matthews Correlation Coefficient RNAshapes: 0.705 PPfold(seed): 0.380 Sensitivity RNAshapes: 0.705 PPfold(seed): 0.170 Positive Predictive Value RNAshapes: 0.709 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	18 PPfold(seed) vs RNASampler(seed) Matthews Correlation Coefficient PPfold(seed): 0.686 RNASampler(seed): 0.486 Sensitivity PPfold(seed): 0.555 RNASampler(seed): 0.345 Positive Predictive Value PPfold(seed): 0.852 RNASampler(seed): 0.693 Number of pairs reference - predicted secondary structure: 18 Wilcoxon single-rank test P-value: 2.66715895098e-08	25 Afold vs PPfold(seed) Matthews Correlation Coefficient Afold: 0.665 PPfold(seed): 0.472 Sensitivity Afold: 0.649 PPfold(seed): 0.263 Positive Predictive Value Afold: 0.686 PPfold(seed): 0.854 Number of pairs reference - predicted secondary structure: 25 Wilcoxon single-rank test P-value: 5.1503931209e-08	30 Pknots vs PPfold(seed) Matthews Correlation Coefficient Pknots: 0.646 PPfold(seed): 0.488 Sensitivity Pknots: 0.645 PPfold(seed): 0.281 Positive Predictive Value Pknots: 0.653 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	40 McQFold vs PPfold(seed) Matthews Correlation Coefficient McQFold: 0.672 PPfold(seed): 0.380 Sensitivity McQFold: 0.651 PPfold(seed): 0.170 Positive Predictive Value McQFold: 0.697 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	23 Carnac(20) vs PPfold(seed) Matthews Correlation Coefficient Carnac(20): 0.496 PPfold(seed): 0.344 Sensitivity Carnac(20): 0.287 PPfold(seed): 0.128 Positive Predictive Value Carnac(20): 0.863 PPfold(seed): 0.927 Number of pairs reference - predicted secondary structure: 23 Wilcoxon single-rank test P-value: 4.94031556815e-08	40 RNASLOpt vs PPfold(seed) Matthews Correlation Coefficient RNASLOpt: 0.649 PPfold(seed): 0.380 Sensitivity RNASLOpt: 0.595 PPfold(seed): 0.170 Positive Predictive Value RNASLOpt: 0.714 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 Cylofold vs PPfold(seed) Matthews Correlation Coefficient Cylofold: 0.624 PPfold(seed): 0.375 Sensitivity Cylofold: 0.593 PPfold(seed): 0.167 Positive Predictive Value Cylofold: 0.661 PPfold(seed): 0.845 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 PPfold(seed) vs Multilign(seed) Matthews Correlation Coefficient PPfold(seed): 0.614 Multilign(seed): 0.485 Sensitivity PPfold(seed): 0.460 Multilign(seed): 0.386 Positive Predictive Value PPfold(seed): 0.825 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.06323189071e-08	40 RNAwolf vs PPfold(seed) Matthews Correlation Coefficient RNAwolf: 0.615 PPfold(seed): 0.380 Sensitivity RNAwolf: 0.619 PPfold(seed): 0.170 Positive Predictive Value RNAwolf: 0.617 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ PPfold(seed) vs Murlet(seed) Matthews Correlation Coefficient PPfold(seed): 0.583 Murlet(seed): 0.490 Sensitivity PPfold(seed): 0.402 Murlet(seed): 0.294 Positive Predictive Value PPfold(seed): 0.852 Murlet(seed): 0.826 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.10776592382e-08	- Alterna vs PPfold(seed) Matthews Correlation Coefficient Alterna: 0.543 PPfold(seed): 0.501 Sensitivity Alterna: 0.529 PPfold(seed): 0.297 Positive Predictive Value Alterna: 0.565 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.54865340847e-08	+ PPfold(seed) vs Carnac(seed) Matthews Correlation Coefficient PPfold(seed): 0.389 Carnac(seed): 0.361 Sensitivity PPfold(seed): 0.179 Carnac(seed): 0.137 Positive Predictive Value PPfold(seed): 0.852 Carnac(seed): 0.952 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ PPfold(seed) vs Vsfold4 Matthews Correlation Coefficient PPfold(seed): 0.380 Vsfold4: 0.333 Sensitivity PPfold(seed): 0.170 Vsfold4: 0.305 Positive Predictive Value PPfold(seed): 0.852 Vsfold4: 0.372 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	= PPfold(seed) vs RSpredict(seed) Matthews Correlation Coefficient PPfold(seed): 0.380 RSpredict(seed): 0.375 Sensitivity PPfold(seed): 0.170 RSpredict(seed): 0.254 Positive Predictive Value PPfold(seed): 0.852 RSpredict(seed): 0.563 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 0.00476252034473	+ PPfold(seed) vs Vsfold5 Matthews Correlation Coefficient PPfold(seed): 0.380 Vsfold5: 0.316 Sensitivity PPfold(seed): 0.170 Vsfold5: 0.290 Positive Predictive Value PPfold(seed): 0.852 Vsfold5: 0.354 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RDfolder vs PPfold(seed) Matthews Correlation Coefficient RDfolder: 0.528 PPfold(seed): 0.501 Sensitivity RDfolder: 0.462 PPfold(seed): 0.297 Positive Predictive Value RDfolder: 0.612 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 4.8721359809e-07	= MCFold vs PPfold(seed) Matthews Correlation Coefficient MCFold: 0.421 PPfold(seed): 0.417 Sensitivity MCFold: 0.478 PPfold(seed): 0.206 Positive Predictive Value MCFold: 0.378 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 0.313407754584	? PPfold(seed) vs NanoFolder Matthews Correlation Coefficient PPfold(seed): 0.497 NanoFolder: 0.474 Sensitivity PPfold(seed): 0.276 NanoFolder: 0.518 Positive Predictive Value PPfold(seed): 0.902 NanoFolder: 0.442 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	+ PPfold(seed) vs Mastr(seed) Matthews Correlation Coefficient PPfold(seed): 0.380 Mastr(seed): 0.299 Sensitivity PPfold(seed): 0.170 Mastr(seed): 0.120 Positive Predictive Value PPfold(seed): 0.852 Mastr(seed): 0.753 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08
Murlet(seed)	91 ContextFold vs Murlet(seed) Matthews Correlation Coefficient ContextFold: 0.718 Murlet(seed): 0.468 Sensitivity ContextFold: 0.666 Murlet(seed): 0.266 Positive Predictive Value ContextFold: 0.777 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 TurboFold(20) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(20): 0.790 Murlet(seed): 0.636 Sensitivity TurboFold(20): 0.734 Murlet(seed): 0.428 Positive Predictive Value TurboFold(20): 0.855 Murlet(seed): 0.952 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	91 CentroidAlifold(seed) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.810 Murlet(seed): 0.468 Sensitivity CentroidAlifold(seed): 0.679 Murlet(seed): 0.266 Positive Predictive Value CentroidAlifold(seed): 0.968 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	91 CentroidHomfold‑LAST vs Murlet(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.731 Murlet(seed): 0.468 Sensitivity CentroidHomfold‑LAST: 0.658 Murlet(seed): 0.266 Positive Predictive Value CentroidHomfold‑LAST: 0.814 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	91 PETfold_pre2.0(seed) vs Murlet(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.743 Murlet(seed): 0.468 Sensitivity PETfold_pre2.0(seed): 0.641 Murlet(seed): 0.266 Positive Predictive Value PETfold_pre2.0(seed): 0.863 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 TurboFold(seed) vs Murlet(seed) Matthews Correlation Coefficient TurboFold(seed): 0.755 Murlet(seed): 0.468 Sensitivity TurboFold(seed): 0.706 Murlet(seed): 0.269 Positive Predictive Value TurboFold(seed): 0.812 Murlet(seed): 0.819 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.23657817852e-08	91 MXScarna(seed) vs Murlet(seed) Matthews Correlation Coefficient MXScarna(seed): 0.712 Murlet(seed): 0.468 Sensitivity MXScarna(seed): 0.676 Murlet(seed): 0.266 Positive Predictive Value MXScarna(seed): 0.754 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 CentroidAlifold(20) vs Murlet(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.788 Murlet(seed): 0.636 Sensitivity CentroidAlifold(20): 0.679 Murlet(seed): 0.428 Positive Predictive Value CentroidAlifold(20): 0.919 Murlet(seed): 0.952 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 PETfold_pre2.0(20) vs Murlet(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.707 Murlet(seed): 0.636 Sensitivity PETfold_pre2.0(20): 0.578 Murlet(seed): 0.428 Positive Predictive Value PETfold_pre2.0(20): 0.871 Murlet(seed): 0.952 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 MXScarna(20) vs Murlet(seed) Matthews Correlation Coefficient MXScarna(20): 0.834 Murlet(seed): 0.636 Sensitivity MXScarna(20): 0.795 Murlet(seed): 0.428 Positive Predictive Value MXScarna(20): 0.877 Murlet(seed): 0.952 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 PPfold(20) vs Murlet(seed) Matthews Correlation Coefficient PPfold(20): 0.664 Murlet(seed): 0.636 Sensitivity PPfold(20): 0.505 Murlet(seed): 0.428 Positive Predictive Value PPfold(20): 0.879 Murlet(seed): 0.952 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 4.83792096436e-08	44 RNAalifold(20) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(20): 0.637 Murlet(seed): 0.636 Sensitivity RNAalifold(20): 0.475 Murlet(seed): 0.428 Positive Predictive Value RNAalifold(20): 0.861 Murlet(seed): 0.952 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 0.667107250991	44 RSpredict(20) vs Murlet(seed) Matthews Correlation Coefficient RSpredict(20): 0.742 Murlet(seed): 0.636 Sensitivity RSpredict(20): 0.662 Murlet(seed): 0.428 Positive Predictive Value RSpredict(20): 0.838 Murlet(seed): 0.952 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	91 IPknot vs Murlet(seed) Matthews Correlation Coefficient IPknot: 0.662 Murlet(seed): 0.468 Sensitivity IPknot: 0.604 Murlet(seed): 0.266 Positive Predictive Value IPknot: 0.730 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 Multilign(20) vs Murlet(seed) Matthews Correlation Coefficient Multilign(20): 0.673 Murlet(seed): 0.636 Sensitivity Multilign(20): 0.523 Murlet(seed): 0.428 Positive Predictive Value Multilign(20): 0.872 Murlet(seed): 0.952 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	91 CentroidFold vs Murlet(seed) Matthews Correlation Coefficient CentroidFold: 0.638 Murlet(seed): 0.468 Sensitivity CentroidFold: 0.560 Murlet(seed): 0.266 Positive Predictive Value CentroidFold: 0.730 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	91 Contrafold vs Murlet(seed) Matthews Correlation Coefficient Contrafold: 0.633 Murlet(seed): 0.468 Sensitivity Contrafold: 0.589 Murlet(seed): 0.266 Positive Predictive Value Contrafold: 0.684 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 Murlet(seed) vs RNASampler(20) Matthews Correlation Coefficient Murlet(seed): 0.636 RNASampler(20): 0.621 Sensitivity Murlet(seed): 0.428 RNASampler(20): 0.426 Positive Predictive Value Murlet(seed): 0.952 RNASampler(20): 0.912 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 2.63254822069e-07	44 Murlet(20) vs Murlet(seed) Matthews Correlation Coefficient Murlet(20): 0.662 Murlet(seed): 0.636 Sensitivity Murlet(20): 0.490 Murlet(seed): 0.428 Positive Predictive Value Murlet(20): 0.900 Murlet(seed): 0.952 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 1.54918844895e-07	78 CMfinder(seed) vs Murlet(seed) Matthews Correlation Coefficient CMfinder(seed): 0.571 Murlet(seed): 0.488 Sensitivity CMfinder(seed): 0.439 Murlet(seed): 0.291 Positive Predictive Value CMfinder(seed): 0.747 Murlet(seed): 0.824 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	91 MaxExpect vs Murlet(seed) Matthews Correlation Coefficient MaxExpect: 0.636 Murlet(seed): 0.468 Sensitivity MaxExpect: 0.602 Murlet(seed): 0.266 Positive Predictive Value MaxExpect: 0.676 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 CMfinder(20) vs Murlet(seed) Matthews Correlation Coefficient CMfinder(20): 0.745 Murlet(seed): 0.636 Sensitivity CMfinder(20): 0.621 Murlet(seed): 0.428 Positive Predictive Value CMfinder(20): 0.899 Murlet(seed): 0.952 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	91 CRWrnafold vs Murlet(seed) Matthews Correlation Coefficient CRWrnafold: 0.516 Murlet(seed): 0.468 Sensitivity CRWrnafold: 0.496 Murlet(seed): 0.266 Positive Predictive Value CRWrnafold: 0.543 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	91 ProbKnot vs Murlet(seed) Matthews Correlation Coefficient ProbKnot: 0.615 Murlet(seed): 0.468 Sensitivity ProbKnot: 0.591 Murlet(seed): 0.266 Positive Predictive Value ProbKnot: 0.646 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 Mastr(20) vs Murlet(seed) Matthews Correlation Coefficient Mastr(20): 0.743 Murlet(seed): 0.636 Sensitivity Mastr(20): 0.664 Murlet(seed): 0.428 Positive Predictive Value Mastr(20): 0.837 Murlet(seed): 0.952 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	91 Fold vs Murlet(seed) Matthews Correlation Coefficient Fold: 0.620 Murlet(seed): 0.468 Sensitivity Fold: 0.599 Murlet(seed): 0.266 Positive Predictive Value Fold: 0.645 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	91 UNAFold vs Murlet(seed) Matthews Correlation Coefficient UNAFold: 0.628 Murlet(seed): 0.468 Sensitivity UNAFold: 0.604 Murlet(seed): 0.266 Positive Predictive Value UNAFold: 0.657 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	91 PknotsRG vs Murlet(seed) Matthews Correlation Coefficient PknotsRG: 0.649 Murlet(seed): 0.468 Sensitivity PknotsRG: 0.635 Murlet(seed): 0.266 Positive Predictive Value PknotsRG: 0.668 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	91 Sfold vs Murlet(seed) Matthews Correlation Coefficient Sfold: 0.599 Murlet(seed): 0.468 Sensitivity Sfold: 0.552 Murlet(seed): 0.266 Positive Predictive Value Sfold: 0.654 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	91 RNAalifold(seed) vs Murlet(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.644 Murlet(seed): 0.468 Sensitivity RNAalifold(seed): 0.479 Murlet(seed): 0.266 Positive Predictive Value RNAalifold(seed): 0.871 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	91 RNAsubopt vs Murlet(seed) Matthews Correlation Coefficient RNAsubopt: 0.579 Murlet(seed): 0.468 Sensitivity RNAsubopt: 0.563 Murlet(seed): 0.266 Positive Predictive Value RNAsubopt: 0.601 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	88 HotKnots vs Murlet(seed) Matthews Correlation Coefficient HotKnots: 0.570 Murlet(seed): 0.483 Sensitivity HotKnots: 0.560 Murlet(seed): 0.283 Positive Predictive Value HotKnots: 0.586 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 88 Wilcoxon single-rank test P-value: 3.56938820447e-08	91 RNAfold vs Murlet(seed) Matthews Correlation Coefficient RNAfold: 0.596 Murlet(seed): 0.468 Sensitivity RNAfold: 0.576 Murlet(seed): 0.266 Positive Predictive Value RNAfold: 0.622 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	91 RNAshapes vs Murlet(seed) Matthews Correlation Coefficient RNAshapes: 0.592 Murlet(seed): 0.468 Sensitivity RNAshapes: 0.572 Murlet(seed): 0.266 Positive Predictive Value RNAshapes: 0.617 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	86 RNASampler(seed) vs Murlet(seed) Matthews Correlation Coefficient RNASampler(seed): 0.557 Murlet(seed): 0.473 Sensitivity RNASampler(seed): 0.389 Murlet(seed): 0.276 Positive Predictive Value RNASampler(seed): 0.802 Murlet(seed): 0.818 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	82 Afold vs Murlet(seed) Matthews Correlation Coefficient Afold: 0.613 Murlet(seed): 0.481 Sensitivity Afold: 0.596 Murlet(seed): 0.275 Positive Predictive Value Afold: 0.634 Murlet(seed): 0.846 Number of pairs reference - predicted secondary structure: 82 Wilcoxon single-rank test P-value: 3.56938820447e-08	71 Murlet(seed) vs Pknots Matthews Correlation Coefficient Murlet(seed): 0.451 Pknots: 0.444 Sensitivity Murlet(seed): 0.267 Pknots: 0.428 Positive Predictive Value Murlet(seed): 0.771 Pknots: 0.471 Number of pairs reference - predicted secondary structure: 71 Wilcoxon single-rank test P-value: 0.0239370604239	91 McQFold vs Murlet(seed) Matthews Correlation Coefficient McQFold: 0.561 Murlet(seed): 0.468 Sensitivity McQFold: 0.518 Murlet(seed): 0.266 Positive Predictive Value McQFold: 0.612 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	44 Murlet(seed) vs Carnac(20) Matthews Correlation Coefficient Murlet(seed): 0.636 Carnac(20): 0.446 Sensitivity Murlet(seed): 0.428 Carnac(20): 0.224 Positive Predictive Value Murlet(seed): 0.952 Carnac(20): 0.896 Number of pairs reference - predicted secondary structure: 44 Wilcoxon single-rank test P-value: 3.56938820447e-08	91 RNASLOpt vs Murlet(seed) Matthews Correlation Coefficient RNASLOpt: 0.546 Murlet(seed): 0.468 Sensitivity RNASLOpt: 0.480 Murlet(seed): 0.266 Positive Predictive Value RNASLOpt: 0.625 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	80 Cylofold vs Murlet(seed) Matthews Correlation Coefficient Cylofold: 0.516 Murlet(seed): 0.505 Sensitivity Cylofold: 0.469 Murlet(seed): 0.315 Positive Predictive Value Cylofold: 0.577 Murlet(seed): 0.817 Number of pairs reference - predicted secondary structure: 80 Wilcoxon single-rank test P-value: 9.18042150391e-06	13 Multilign(seed) vs Murlet(seed) Matthews Correlation Coefficient Multilign(seed): 0.485 Murlet(seed): 0.448 Sensitivity Multilign(seed): 0.386 Murlet(seed): 0.284 Positive Predictive Value Multilign(seed): 0.619 Murlet(seed): 0.718 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.96907987703e-08	91 Murlet(seed) vs RNAwolf Matthews Correlation Coefficient Murlet(seed): 0.468 RNAwolf: 0.407 Sensitivity Murlet(seed): 0.266 RNAwolf: 0.405 Positive Predictive Value Murlet(seed): 0.828 RNAwolf: 0.415 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	21 PPfold(seed) vs Murlet(seed) Matthews Correlation Coefficient PPfold(seed): 0.583 Murlet(seed): 0.490 Sensitivity PPfold(seed): 0.402 Murlet(seed): 0.294 Positive Predictive Value PPfold(seed): 0.852 Murlet(seed): 0.826 Number of pairs reference - predicted secondary structure: 21 Wilcoxon single-rank test P-value: 5.10776592382e-08		= Alterna vs Murlet(seed) Matthews Correlation Coefficient Alterna: 0.456 Murlet(seed): 0.451 Sensitivity Alterna: 0.430 Murlet(seed): 0.267 Positive Predictive Value Alterna: 0.494 Murlet(seed): 0.771 Number of pairs reference - predicted secondary structure: 71 Wilcoxon single-rank test P-value: 0.00911763231782	+ Murlet(seed) vs Carnac(seed) Matthews Correlation Coefficient Murlet(seed): 0.468 Carnac(seed): 0.428 Sensitivity Murlet(seed): 0.266 Carnac(seed): 0.217 Positive Predictive Value Murlet(seed): 0.828 Carnac(seed): 0.852 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(seed) vs Vsfold4 Matthews Correlation Coefficient Murlet(seed): 0.468 Vsfold4: 0.402 Sensitivity Murlet(seed): 0.266 Vsfold4: 0.357 Positive Predictive Value Murlet(seed): 0.828 Vsfold4: 0.461 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RSpredict(seed) vs Murlet(seed) Matthews Correlation Coefficient RSpredict(seed): 0.491 Murlet(seed): 0.468 Sensitivity RSpredict(seed): 0.380 Murlet(seed): 0.266 Positive Predictive Value RSpredict(seed): 0.641 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(seed) vs Vsfold5 Matthews Correlation Coefficient Murlet(seed): 0.468 Vsfold5: 0.363 Sensitivity Murlet(seed): 0.266 Vsfold5: 0.328 Positive Predictive Value Murlet(seed): 0.828 Vsfold5: 0.409 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Murlet(seed) vs RDfolder Matthews Correlation Coefficient Murlet(seed): 0.451 RDfolder: 0.361 Sensitivity Murlet(seed): 0.267 RDfolder: 0.294 Positive Predictive Value Murlet(seed): 0.771 RDfolder: 0.455 Number of pairs reference - predicted secondary structure: 71 Wilcoxon single-rank test P-value: 3.56938820447e-08	= Murlet(seed) vs MCFold Matthews Correlation Coefficient Murlet(seed): 0.431 MCFold: 0.427 Sensitivity Murlet(seed): 0.236 MCFold: 0.470 Positive Predictive Value Murlet(seed): 0.793 MCFold: 0.396 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 0.221270004692	+ Murlet(seed) vs NanoFolder Matthews Correlation Coefficient Murlet(seed): 0.441 NanoFolder: 0.421 Sensitivity Murlet(seed): 0.213 NanoFolder: 0.471 Positive Predictive Value Murlet(seed): 0.921 NanoFolder: 0.385 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 0.000616773583101	= Murlet(seed) vs Mastr(seed) Matthews Correlation Coefficient Murlet(seed): 0.468 Mastr(seed): 0.467 Sensitivity Murlet(seed): 0.266 Mastr(seed): 0.278 Positive Predictive Value Murlet(seed): 0.828 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 0.0563054219211
Alterna	693 ContextFold vs Alterna Matthews Correlation Coefficient ContextFold: 0.765 Alterna: 0.552 Sensitivity ContextFold: 0.723 Alterna: 0.547 Positive Predictive Value ContextFold: 0.814 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	211 TurboFold(20) vs Alterna Matthews Correlation Coefficient TurboFold(20): 0.913 Alterna: 0.618 Sensitivity TurboFold(20): 0.887 Alterna: 0.626 Positive Predictive Value TurboFold(20): 0.940 Alterna: 0.616 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	145 CentroidAlifold(seed) vs Alterna Matthews Correlation Coefficient CentroidAlifold(seed): 0.781 Alterna: 0.558 Sensitivity CentroidAlifold(seed): 0.674 Alterna: 0.548 Positive Predictive Value CentroidAlifold(seed): 0.908 Alterna: 0.575 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 CentroidHomfold‑LAST vs Alterna Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.748 Alterna: 0.552 Sensitivity CentroidHomfold‑LAST: 0.687 Alterna: 0.547 Positive Predictive Value CentroidHomfold‑LAST: 0.818 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	360 PETfold_pre2.0(seed) vs Alterna Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.909 Alterna: 0.585 Sensitivity PETfold_pre2.0(seed): 0.870 Alterna: 0.595 Positive Predictive Value PETfold_pre2.0(seed): 0.950 Alterna: 0.582 Number of pairs reference - predicted secondary structure: 360 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 TurboFold(seed) vs Alterna Matthews Correlation Coefficient TurboFold(seed): 0.720 Alterna: 0.546 Sensitivity TurboFold(seed): 0.663 Alterna: 0.520 Positive Predictive Value TurboFold(seed): 0.786 Alterna: 0.581 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.23657817852e-08	156 MXScarna(seed) vs Alterna Matthews Correlation Coefficient MXScarna(seed): 0.749 Alterna: 0.560 Sensitivity MXScarna(seed): 0.715 Alterna: 0.552 Positive Predictive Value MXScarna(seed): 0.788 Alterna: 0.575 Number of pairs reference - predicted secondary structure: 156 Wilcoxon single-rank test P-value: 3.56938820447e-08	211 CentroidAlifold(20) vs Alterna Matthews Correlation Coefficient CentroidAlifold(20): 0.907 Alterna: 0.618 Sensitivity CentroidAlifold(20): 0.844 Alterna: 0.626 Positive Predictive Value CentroidAlifold(20): 0.977 Alterna: 0.616 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	211 PETfold_pre2.0(20) vs Alterna Matthews Correlation Coefficient PETfold_pre2.0(20): 0.887 Alterna: 0.618 Sensitivity PETfold_pre2.0(20): 0.811 Alterna: 0.626 Positive Predictive Value PETfold_pre2.0(20): 0.973 Alterna: 0.616 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	211 MXScarna(20) vs Alterna Matthews Correlation Coefficient MXScarna(20): 0.873 Alterna: 0.618 Sensitivity MXScarna(20): 0.835 Alterna: 0.626 Positive Predictive Value MXScarna(20): 0.915 Alterna: 0.616 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	208 PPfold(20) vs Alterna Matthews Correlation Coefficient PPfold(20): 0.884 Alterna: 0.618 Sensitivity PPfold(20): 0.800 Alterna: 0.626 Positive Predictive Value PPfold(20): 0.979 Alterna: 0.616 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	211 RNAalifold(20) vs Alterna Matthews Correlation Coefficient RNAalifold(20): 0.883 Alterna: 0.618 Sensitivity RNAalifold(20): 0.795 Alterna: 0.626 Positive Predictive Value RNAalifold(20): 0.982 Alterna: 0.616 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	211 RSpredict(20) vs Alterna Matthews Correlation Coefficient RSpredict(20): 0.821 Alterna: 0.618 Sensitivity RSpredict(20): 0.738 Alterna: 0.626 Positive Predictive Value RSpredict(20): 0.917 Alterna: 0.616 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 IPknot vs Alterna Matthews Correlation Coefficient IPknot: 0.689 Alterna: 0.552 Sensitivity IPknot: 0.655 Alterna: 0.547 Positive Predictive Value IPknot: 0.731 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 Multilign(20) vs Alterna Matthews Correlation Coefficient Multilign(20): 0.829 Alterna: 0.616 Sensitivity Multilign(20): 0.758 Alterna: 0.624 Positive Predictive Value Multilign(20): 0.910 Alterna: 0.614 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 CentroidFold vs Alterna Matthews Correlation Coefficient CentroidFold: 0.658 Alterna: 0.552 Sensitivity CentroidFold: 0.621 Alterna: 0.547 Positive Predictive Value CentroidFold: 0.703 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 Contrafold vs Alterna Matthews Correlation Coefficient Contrafold: 0.657 Alterna: 0.552 Sensitivity Contrafold: 0.646 Alterna: 0.547 Positive Predictive Value Contrafold: 0.675 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	208 RNASampler(20) vs Alterna Matthews Correlation Coefficient RNASampler(20): 0.859 Alterna: 0.620 Sensitivity RNASampler(20): 0.761 Alterna: 0.627 Positive Predictive Value RNASampler(20): 0.971 Alterna: 0.618 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	211 Murlet(20) vs Alterna Matthews Correlation Coefficient Murlet(20): 0.780 Alterna: 0.618 Sensitivity Murlet(20): 0.685 Alterna: 0.626 Positive Predictive Value Murlet(20): 0.892 Alterna: 0.616 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	62 CMfinder(seed) vs Alterna Matthews Correlation Coefficient CMfinder(seed): 0.512 Alterna: 0.405 Sensitivity CMfinder(seed): 0.382 Alterna: 0.380 Positive Predictive Value CMfinder(seed): 0.696 Alterna: 0.445 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 MaxExpect vs Alterna Matthews Correlation Coefficient MaxExpect: 0.641 Alterna: 0.552 Sensitivity MaxExpect: 0.622 Alterna: 0.547 Positive Predictive Value MaxExpect: 0.667 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	211 CMfinder(20) vs Alterna Matthews Correlation Coefficient CMfinder(20): 0.792 Alterna: 0.618 Sensitivity CMfinder(20): 0.679 Alterna: 0.626 Positive Predictive Value CMfinder(20): 0.927 Alterna: 0.616 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	692 CRWrnafold vs Alterna Matthews Correlation Coefficient CRWrnafold: 0.615 Alterna: 0.552 Sensitivity CRWrnafold: 0.601 Alterna: 0.546 Positive Predictive Value CRWrnafold: 0.635 Alterna: 0.565 Number of pairs reference - predicted secondary structure: 692 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 ProbKnot vs Alterna Matthews Correlation Coefficient ProbKnot: 0.640 Alterna: 0.552 Sensitivity ProbKnot: 0.632 Alterna: 0.547 Positive Predictive Value ProbKnot: 0.656 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	211 Mastr(20) vs Alterna Matthews Correlation Coefficient Mastr(20): 0.730 Alterna: 0.618 Sensitivity Mastr(20): 0.677 Alterna: 0.626 Positive Predictive Value Mastr(20): 0.790 Alterna: 0.616 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 Fold vs Alterna Matthews Correlation Coefficient Fold: 0.633 Alterna: 0.552 Sensitivity Fold: 0.623 Alterna: 0.547 Positive Predictive Value Fold: 0.650 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 UNAFold vs Alterna Matthews Correlation Coefficient UNAFold: 0.597 Alterna: 0.552 Sensitivity UNAFold: 0.584 Alterna: 0.547 Positive Predictive Value UNAFold: 0.617 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 PknotsRG vs Alterna Matthews Correlation Coefficient PknotsRG: 0.605 Alterna: 0.552 Sensitivity PknotsRG: 0.598 Alterna: 0.547 Positive Predictive Value PknotsRG: 0.619 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 Sfold vs Alterna Matthews Correlation Coefficient Sfold: 0.603 Alterna: 0.552 Sensitivity Sfold: 0.566 Alterna: 0.547 Positive Predictive Value Sfold: 0.649 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	134 RNAalifold(seed) vs Alterna Matthews Correlation Coefficient RNAalifold(seed): 0.617 Alterna: 0.554 Sensitivity RNAalifold(seed): 0.418 Alterna: 0.541 Positive Predictive Value RNAalifold(seed): 0.917 Alterna: 0.575 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 RNAsubopt vs Alterna Matthews Correlation Coefficient RNAsubopt: 0.608 Alterna: 0.552 Sensitivity RNAsubopt: 0.603 Alterna: 0.547 Positive Predictive Value RNAsubopt: 0.621 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 HotKnots vs Alterna Matthews Correlation Coefficient HotKnots: 0.594 Alterna: 0.552 Sensitivity HotKnots: 0.590 Alterna: 0.547 Positive Predictive Value HotKnots: 0.605 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 RNAfold vs Alterna Matthews Correlation Coefficient RNAfold: 0.596 Alterna: 0.552 Sensitivity RNAfold: 0.589 Alterna: 0.547 Positive Predictive Value RNAfold: 0.611 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 RNAshapes vs Alterna Matthews Correlation Coefficient RNAshapes: 0.596 Alterna: 0.552 Sensitivity RNAshapes: 0.587 Alterna: 0.547 Positive Predictive Value RNAshapes: 0.612 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	69 RNASampler(seed) vs Alterna Matthews Correlation Coefficient RNASampler(seed): 0.455 Alterna: 0.449 Sensitivity RNASampler(seed): 0.284 Alterna: 0.422 Positive Predictive Value RNASampler(seed): 0.738 Alterna: 0.490 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 0.000167509336666	402 Afold vs Alterna Matthews Correlation Coefficient Afold: 0.542 Alterna: 0.531 Sensitivity Afold: 0.522 Alterna: 0.509 Positive Predictive Value Afold: 0.574 Alterna: 0.565 Number of pairs reference - predicted secondary structure: 402 Wilcoxon single-rank test P-value: 3.85233844192e-08	693 Pknots vs Alterna Matthews Correlation Coefficient Pknots: 0.610 Alterna: 0.552 Sensitivity Pknots: 0.599 Alterna: 0.547 Positive Predictive Value Pknots: 0.629 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 McQFold vs Alterna Matthews Correlation Coefficient McQFold: 0.653 Alterna: 0.552 Sensitivity McQFold: 0.624 Alterna: 0.547 Positive Predictive Value McQFold: 0.689 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	211 Carnac(20) vs Alterna Matthews Correlation Coefficient Carnac(20): 0.744 Alterna: 0.618 Sensitivity Carnac(20): 0.591 Alterna: 0.626 Positive Predictive Value Carnac(20): 0.940 Alterna: 0.616 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 RNASLOpt vs Alterna Matthews Correlation Coefficient RNASLOpt: 0.612 Alterna: 0.552 Sensitivity RNASLOpt: 0.567 Alterna: 0.547 Positive Predictive Value RNASLOpt: 0.667 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	673 Cylofold vs Alterna Matthews Correlation Coefficient Cylofold: 0.621 Alterna: 0.555 Sensitivity Cylofold: 0.599 Alterna: 0.549 Positive Predictive Value Cylofold: 0.650 Alterna: 0.569 Number of pairs reference - predicted secondary structure: 673 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Multilign(seed) vs Alterna Matthews Correlation Coefficient Multilign(seed): 0.485 Alterna: 0.420 Sensitivity Multilign(seed): 0.386 Alterna: 0.391 Positive Predictive Value Multilign(seed): 0.619 Alterna: 0.462 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.36983135185e-08	693 Alterna vs RNAwolf Matthews Correlation Coefficient Alterna: 0.552 RNAwolf: 0.551 Sensitivity Alterna: 0.547 RNAwolf: 0.555 Positive Predictive Value Alterna: 0.566 RNAwolf: 0.555 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 0.808824058118	29 Alterna vs PPfold(seed) Matthews Correlation Coefficient Alterna: 0.543 PPfold(seed): 0.501 Sensitivity Alterna: 0.529 PPfold(seed): 0.297 Positive Predictive Value Alterna: 0.565 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 5.54865340847e-08	71 Alterna vs Murlet(seed) Matthews Correlation Coefficient Alterna: 0.456 Murlet(seed): 0.451 Sensitivity Alterna: 0.430 Murlet(seed): 0.267 Positive Predictive Value Alterna: 0.494 Murlet(seed): 0.771 Number of pairs reference - predicted secondary structure: 71 Wilcoxon single-rank test P-value: 0.00911763231782		+ Alterna vs Carnac(seed) Matthews Correlation Coefficient Alterna: 0.507 Carnac(seed): 0.503 Sensitivity Alterna: 0.485 Carnac(seed): 0.281 Positive Predictive Value Alterna: 0.538 Carnac(seed): 0.907 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 0.000387428335855	- Vsfold4 vs Alterna Matthews Correlation Coefficient Vsfold4: 0.596 Alterna: 0.552 Sensitivity Vsfold4: 0.547 Alterna: 0.547 Positive Predictive Value Vsfold4: 0.656 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Alterna vs RSpredict(seed) Matthews Correlation Coefficient Alterna: 0.558 RSpredict(seed): 0.472 Sensitivity Alterna: 0.548 RSpredict(seed): 0.337 Positive Predictive Value Alterna: 0.575 RSpredict(seed): 0.669 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	- Vsfold5 vs Alterna Matthews Correlation Coefficient Vsfold5: 0.582 Alterna: 0.552 Sensitivity Vsfold5: 0.551 Alterna: 0.547 Positive Predictive Value Vsfold5: 0.623 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Alterna vs RDfolder Matthews Correlation Coefficient Alterna: 0.552 RDfolder: 0.520 Sensitivity Alterna: 0.547 RDfolder: 0.464 Positive Predictive Value Alterna: 0.566 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Alterna vs MCFold Matthews Correlation Coefficient Alterna: 0.552 MCFold: 0.468 Sensitivity Alterna: 0.543 MCFold: 0.524 Positive Predictive Value Alterna: 0.569 MCFold: 0.428 Number of pairs reference - predicted secondary structure: 649 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Alterna vs NanoFolder Matthews Correlation Coefficient Alterna: 0.573 NanoFolder: 0.390 Sensitivity Alterna: 0.561 NanoFolder: 0.447 Positive Predictive Value Alterna: 0.593 NanoFolder: 0.350 Number of pairs reference - predicted secondary structure: 87 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Alterna vs Mastr(seed) Matthews Correlation Coefficient Alterna: 0.560 Mastr(seed): 0.309 Sensitivity Alterna: 0.552 Mastr(seed): 0.118 Positive Predictive Value Alterna: 0.575 Mastr(seed): 0.815 Number of pairs reference - predicted secondary structure: 157 Wilcoxon single-rank test P-value: 3.56938820447e-08
Carnac(seed)	123 ContextFold vs Carnac(seed) Matthews Correlation Coefficient ContextFold: 0.787 Carnac(seed): 0.415 Sensitivity ContextFold: 0.744 Carnac(seed): 0.196 Positive Predictive Value ContextFold: 0.835 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	68 TurboFold(20) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(20): 0.834 Carnac(seed): 0.431 Sensitivity TurboFold(20): 0.797 Carnac(seed): 0.206 Positive Predictive Value TurboFold(20): 0.875 Carnac(seed): 0.907 Number of pairs reference - predicted secondary structure: 68 Wilcoxon single-rank test P-value: 3.56938820447e-08	120 CentroidAlifold(seed) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.798 Carnac(seed): 0.424 Sensitivity CentroidAlifold(seed): 0.671 Carnac(seed): 0.205 Positive Predictive Value CentroidAlifold(seed): 0.951 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 120 Wilcoxon single-rank test P-value: 3.56938820447e-08	123 CentroidHomfold‑LAST vs Carnac(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.765 Carnac(seed): 0.415 Sensitivity CentroidHomfold‑LAST: 0.702 Carnac(seed): 0.196 Positive Predictive Value CentroidHomfold‑LAST: 0.838 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	122 PETfold_pre2.0(seed) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.772 Carnac(seed): 0.417 Sensitivity PETfold_pre2.0(seed): 0.676 Carnac(seed): 0.198 Positive Predictive Value PETfold_pre2.0(seed): 0.885 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 122 Wilcoxon single-rank test P-value: 3.56938820447e-08	32 TurboFold(seed) vs Carnac(seed) Matthews Correlation Coefficient TurboFold(seed): 0.790 Carnac(seed): 0.422 Sensitivity TurboFold(seed): 0.759 Carnac(seed): 0.188 Positive Predictive Value TurboFold(seed): 0.826 Carnac(seed): 0.955 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	123 MXScarna(seed) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(seed): 0.742 Carnac(seed): 0.415 Sensitivity MXScarna(seed): 0.707 Carnac(seed): 0.196 Positive Predictive Value MXScarna(seed): 0.782 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	68 CentroidAlifold(20) vs Carnac(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.760 Carnac(seed): 0.431 Sensitivity CentroidAlifold(20): 0.625 Carnac(seed): 0.206 Positive Predictive Value CentroidAlifold(20): 0.928 Carnac(seed): 0.907 Number of pairs reference - predicted secondary structure: 68 Wilcoxon single-rank test P-value: 3.56938820447e-08	68 PETfold_pre2.0(20) vs Carnac(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.692 Carnac(seed): 0.431 Sensitivity PETfold_pre2.0(20): 0.533 Carnac(seed): 0.206 Positive Predictive Value PETfold_pre2.0(20): 0.904 Carnac(seed): 0.907 Number of pairs reference - predicted secondary structure: 68 Wilcoxon single-rank test P-value: 3.56938820447e-08	68 MXScarna(20) vs Carnac(seed) Matthews Correlation Coefficient MXScarna(20): 0.835 Carnac(seed): 0.431 Sensitivity MXScarna(20): 0.786 Carnac(seed): 0.206 Positive Predictive Value MXScarna(20): 0.890 Carnac(seed): 0.907 Number of pairs reference - predicted secondary structure: 68 Wilcoxon single-rank test P-value: 3.56938820447e-08	68 PPfold(20) vs Carnac(seed) Matthews Correlation Coefficient PPfold(20): 0.664 Carnac(seed): 0.431 Sensitivity PPfold(20): 0.485 Carnac(seed): 0.206 Positive Predictive Value PPfold(20): 0.913 Carnac(seed): 0.907 Number of pairs reference - predicted secondary structure: 68 Wilcoxon single-rank test P-value: 3.56938820447e-08	68 RNAalifold(20) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(20): 0.671 Carnac(seed): 0.431 Sensitivity RNAalifold(20): 0.496 Carnac(seed): 0.206 Positive Predictive Value RNAalifold(20): 0.911 Carnac(seed): 0.907 Number of pairs reference - predicted secondary structure: 68 Wilcoxon single-rank test P-value: 3.56938820447e-08	68 RSpredict(20) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(20): 0.759 Carnac(seed): 0.431 Sensitivity RSpredict(20): 0.662 Carnac(seed): 0.206 Positive Predictive Value RSpredict(20): 0.873 Carnac(seed): 0.907 Number of pairs reference - predicted secondary structure: 68 Wilcoxon single-rank test P-value: 3.56938820447e-08	123 IPknot vs Carnac(seed) Matthews Correlation Coefficient IPknot: 0.713 Carnac(seed): 0.415 Sensitivity IPknot: 0.668 Carnac(seed): 0.196 Positive Predictive Value IPknot: 0.764 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	66 Multilign(20) vs Carnac(seed) Matthews Correlation Coefficient Multilign(20): 0.650 Carnac(seed): 0.442 Sensitivity Multilign(20): 0.513 Carnac(seed): 0.217 Positive Predictive Value Multilign(20): 0.829 Carnac(seed): 0.907 Number of pairs reference - predicted secondary structure: 66 Wilcoxon single-rank test P-value: 3.56938820447e-08	123 CentroidFold vs Carnac(seed) Matthews Correlation Coefficient CentroidFold: 0.674 Carnac(seed): 0.415 Sensitivity CentroidFold: 0.611 Carnac(seed): 0.196 Positive Predictive Value CentroidFold: 0.747 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	123 Contrafold vs Carnac(seed) Matthews Correlation Coefficient Contrafold: 0.665 Carnac(seed): 0.415 Sensitivity Contrafold: 0.633 Carnac(seed): 0.196 Positive Predictive Value Contrafold: 0.702 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	68 RNASampler(20) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(20): 0.639 Carnac(seed): 0.431 Sensitivity RNASampler(20): 0.434 Carnac(seed): 0.206 Positive Predictive Value RNASampler(20): 0.946 Carnac(seed): 0.907 Number of pairs reference - predicted secondary structure: 68 Wilcoxon single-rank test P-value: 3.56938820447e-08	67 Murlet(20) vs Carnac(seed) Matthews Correlation Coefficient Murlet(20): 0.664 Carnac(seed): 0.435 Sensitivity Murlet(20): 0.480 Carnac(seed): 0.211 Positive Predictive Value Murlet(20): 0.922 Carnac(seed): 0.907 Number of pairs reference - predicted secondary structure: 67 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 CMfinder(seed) vs Carnac(seed) Matthews Correlation Coefficient CMfinder(seed): 0.571 Carnac(seed): 0.422 Sensitivity CMfinder(seed): 0.439 Carnac(seed): 0.216 Positive Predictive Value CMfinder(seed): 0.747 Carnac(seed): 0.830 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	123 MaxExpect vs Carnac(seed) Matthews Correlation Coefficient MaxExpect: 0.667 Carnac(seed): 0.415 Sensitivity MaxExpect: 0.644 Carnac(seed): 0.196 Positive Predictive Value MaxExpect: 0.695 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	68 CMfinder(20) vs Carnac(seed) Matthews Correlation Coefficient CMfinder(20): 0.717 Carnac(seed): 0.431 Sensitivity CMfinder(20): 0.575 Carnac(seed): 0.206 Positive Predictive Value CMfinder(20): 0.898 Carnac(seed): 0.907 Number of pairs reference - predicted secondary structure: 68 Wilcoxon single-rank test P-value: 3.56938820447e-08	123 CRWrnafold vs Carnac(seed) Matthews Correlation Coefficient CRWrnafold: 0.599 Carnac(seed): 0.415 Sensitivity CRWrnafold: 0.584 Carnac(seed): 0.196 Positive Predictive Value CRWrnafold: 0.618 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	123 ProbKnot vs Carnac(seed) Matthews Correlation Coefficient ProbKnot: 0.651 Carnac(seed): 0.415 Sensitivity ProbKnot: 0.636 Carnac(seed): 0.196 Positive Predictive Value ProbKnot: 0.671 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	68 Mastr(20) vs Carnac(seed) Matthews Correlation Coefficient Mastr(20): 0.741 Carnac(seed): 0.431 Sensitivity Mastr(20): 0.633 Carnac(seed): 0.206 Positive Predictive Value Mastr(20): 0.870 Carnac(seed): 0.907 Number of pairs reference - predicted secondary structure: 68 Wilcoxon single-rank test P-value: 3.56938820447e-08	123 Fold vs Carnac(seed) Matthews Correlation Coefficient Fold: 0.657 Carnac(seed): 0.415 Sensitivity Fold: 0.645 Carnac(seed): 0.196 Positive Predictive Value Fold: 0.673 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	123 UNAFold vs Carnac(seed) Matthews Correlation Coefficient UNAFold: 0.655 Carnac(seed): 0.415 Sensitivity UNAFold: 0.640 Carnac(seed): 0.196 Positive Predictive Value UNAFold: 0.674 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	123 PknotsRG vs Carnac(seed) Matthews Correlation Coefficient PknotsRG: 0.668 Carnac(seed): 0.415 Sensitivity PknotsRG: 0.661 Carnac(seed): 0.196 Positive Predictive Value PknotsRG: 0.679 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	123 Sfold vs Carnac(seed) Matthews Correlation Coefficient Sfold: 0.648 Carnac(seed): 0.415 Sensitivity Sfold: 0.608 Carnac(seed): 0.196 Positive Predictive Value Sfold: 0.695 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	112 RNAalifold(seed) vs Carnac(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.643 Carnac(seed): 0.439 Sensitivity RNAalifold(seed): 0.466 Carnac(seed): 0.219 Positive Predictive Value RNAalifold(seed): 0.892 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 112 Wilcoxon single-rank test P-value: 3.56938820447e-08	123 RNAsubopt vs Carnac(seed) Matthews Correlation Coefficient RNAsubopt: 0.635 Carnac(seed): 0.415 Sensitivity RNAsubopt: 0.625 Carnac(seed): 0.196 Positive Predictive Value RNAsubopt: 0.649 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	120 HotKnots vs Carnac(seed) Matthews Correlation Coefficient HotKnots: 0.619 Carnac(seed): 0.420 Sensitivity HotKnots: 0.615 Carnac(seed): 0.199 Positive Predictive Value HotKnots: 0.628 Carnac(seed): 0.889 Number of pairs reference - predicted secondary structure: 120 Wilcoxon single-rank test P-value: 3.56938820447e-08	123 RNAfold vs Carnac(seed) Matthews Correlation Coefficient RNAfold: 0.639 Carnac(seed): 0.415 Sensitivity RNAfold: 0.628 Carnac(seed): 0.196 Positive Predictive Value RNAfold: 0.656 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	123 RNAshapes vs Carnac(seed) Matthews Correlation Coefficient RNAshapes: 0.632 Carnac(seed): 0.415 Sensitivity RNAshapes: 0.621 Carnac(seed): 0.196 Positive Predictive Value RNAshapes: 0.649 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	86 RNASampler(seed) vs Carnac(seed) Matthews Correlation Coefficient RNASampler(seed): 0.557 Carnac(seed): 0.450 Sensitivity RNASampler(seed): 0.389 Carnac(seed): 0.239 Positive Predictive Value RNASampler(seed): 0.802 Carnac(seed): 0.852 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	102 Afold vs Carnac(seed) Matthews Correlation Coefficient Afold: 0.635 Carnac(seed): 0.447 Sensitivity Afold: 0.622 Carnac(seed): 0.227 Positive Predictive Value Afold: 0.653 Carnac(seed): 0.883 Number of pairs reference - predicted secondary structure: 102 Wilcoxon single-rank test P-value: 3.56938820447e-08	90 Carnac(seed) vs Pknots Matthews Correlation Coefficient Carnac(seed): 0.498 Pknots: 0.484 Sensitivity Carnac(seed): 0.276 Pknots: 0.470 Positive Predictive Value Carnac(seed): 0.907 Pknots: 0.509 Number of pairs reference - predicted secondary structure: 90 Wilcoxon single-rank test P-value: 3.76761760679e-06	123 McQFold vs Carnac(seed) Matthews Correlation Coefficient McQFold: 0.581 Carnac(seed): 0.415 Sensitivity McQFold: 0.545 Carnac(seed): 0.196 Positive Predictive Value McQFold: 0.624 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	68 Carnac(20) vs Carnac(seed) Matthews Correlation Coefficient Carnac(20): 0.523 Carnac(seed): 0.431 Sensitivity Carnac(20): 0.304 Carnac(seed): 0.206 Positive Predictive Value Carnac(20): 0.905 Carnac(seed): 0.907 Number of pairs reference - predicted secondary structure: 68 Wilcoxon single-rank test P-value: 3.56938820447e-08	123 RNASLOpt vs Carnac(seed) Matthews Correlation Coefficient RNASLOpt: 0.569 Carnac(seed): 0.415 Sensitivity RNASLOpt: 0.511 Carnac(seed): 0.196 Positive Predictive Value RNASLOpt: 0.640 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	112 Cylofold vs Carnac(seed) Matthews Correlation Coefficient Cylofold: 0.541 Carnac(seed): 0.408 Sensitivity Cylofold: 0.502 Carnac(seed): 0.189 Positive Predictive Value Cylofold: 0.591 Carnac(seed): 0.888 Number of pairs reference - predicted secondary structure: 112 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Carnac(seed) vs Multilign(seed) Matthews Correlation Coefficient Carnac(seed): 0.566 Multilign(seed): 0.485 Sensitivity Carnac(seed): 0.349 Multilign(seed): 0.386 Positive Predictive Value Carnac(seed): 0.926 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.93248927742e-08	123 RNAwolf vs Carnac(seed) Matthews Correlation Coefficient RNAwolf: 0.472 Carnac(seed): 0.415 Sensitivity RNAwolf: 0.473 Carnac(seed): 0.196 Positive Predictive Value RNAwolf: 0.478 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	38 PPfold(seed) vs Carnac(seed) Matthews Correlation Coefficient PPfold(seed): 0.389 Carnac(seed): 0.361 Sensitivity PPfold(seed): 0.179 Carnac(seed): 0.137 Positive Predictive Value PPfold(seed): 0.852 Carnac(seed): 0.952 Number of pairs reference - predicted secondary structure: 38 Wilcoxon single-rank test P-value: 3.56938820447e-08	91 Murlet(seed) vs Carnac(seed) Matthews Correlation Coefficient Murlet(seed): 0.468 Carnac(seed): 0.428 Sensitivity Murlet(seed): 0.266 Carnac(seed): 0.217 Positive Predictive Value Murlet(seed): 0.828 Carnac(seed): 0.852 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	89 Alterna vs Carnac(seed) Matthews Correlation Coefficient Alterna: 0.507 Carnac(seed): 0.503 Sensitivity Alterna: 0.485 Carnac(seed): 0.281 Positive Predictive Value Alterna: 0.538 Carnac(seed): 0.907 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 0.000387428335855		+ Carnac(seed) vs Vsfold4 Matthews Correlation Coefficient Carnac(seed): 0.415 Vsfold4: 0.379 Sensitivity Carnac(seed): 0.196 Vsfold4: 0.342 Positive Predictive Value Carnac(seed): 0.884 Vsfold4: 0.429 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	- RSpredict(seed) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(seed): 0.439 Carnac(seed): 0.424 Sensitivity RSpredict(seed): 0.318 Carnac(seed): 0.205 Positive Predictive Value RSpredict(seed): 0.611 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 120 Wilcoxon single-rank test P-value: 1.70738736246e-07	+ Carnac(seed) vs Vsfold5 Matthews Correlation Coefficient Carnac(seed): 0.415 Vsfold5: 0.353 Sensitivity Carnac(seed): 0.196 Vsfold5: 0.325 Positive Predictive Value Carnac(seed): 0.884 Vsfold5: 0.392 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Carnac(seed) vs RDfolder Matthews Correlation Coefficient Carnac(seed): 0.503 RDfolder: 0.434 Sensitivity Carnac(seed): 0.281 RDfolder: 0.361 Positive Predictive Value Carnac(seed): 0.907 RDfolder: 0.532 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	= MCFold vs Carnac(seed) Matthews Correlation Coefficient MCFold: 0.446 Carnac(seed): 0.444 Sensitivity MCFold: 0.494 Carnac(seed): 0.222 Positive Predictive Value MCFold: 0.411 Carnac(seed): 0.896 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 0.00911763231782	+ Carnac(seed) vs NanoFolder Matthews Correlation Coefficient Carnac(seed): 0.502 NanoFolder: 0.469 Sensitivity Carnac(seed): 0.263 NanoFolder: 0.526 Positive Predictive Value Carnac(seed): 0.964 NanoFolder: 0.425 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	+ Carnac(seed) vs Mastr(seed) Matthews Correlation Coefficient Carnac(seed): 0.415 Mastr(seed): 0.385 Sensitivity Carnac(seed): 0.196 Mastr(seed): 0.190 Positive Predictive Value Carnac(seed): 0.884 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08
Vsfold4	882 ContextFold vs Vsfold4 Matthews Correlation Coefficient ContextFold: 0.779 Vsfold4: 0.487 Sensitivity ContextFold: 0.741 Vsfold4: 0.447 Positive Predictive Value ContextFold: 0.823 Vsfold4: 0.537 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 TurboFold(20) vs Vsfold4 Matthews Correlation Coefficient TurboFold(20): 0.889 Vsfold4: 0.502 Sensitivity TurboFold(20): 0.861 Vsfold4: 0.466 Positive Predictive Value TurboFold(20): 0.919 Vsfold4: 0.546 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	216 CentroidAlifold(seed) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(seed): 0.790 Vsfold4: 0.355 Sensitivity CentroidAlifold(seed): 0.699 Vsfold4: 0.324 Positive Predictive Value CentroidAlifold(seed): 0.896 Vsfold4: 0.397 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 CentroidHomfold‑LAST vs Vsfold4 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.736 Vsfold4: 0.487 Sensitivity CentroidHomfold‑LAST: 0.665 Vsfold4: 0.447 Positive Predictive Value CentroidHomfold‑LAST: 0.818 Vsfold4: 0.537 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	498 PETfold_pre2.0(seed) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.879 Vsfold4: 0.531 Sensitivity PETfold_pre2.0(seed): 0.825 Vsfold4: 0.496 Positive Predictive Value PETfold_pre2.0(seed): 0.938 Vsfold4: 0.575 Number of pairs reference - predicted secondary structure: 498 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 TurboFold(seed) vs Vsfold4 Matthews Correlation Coefficient TurboFold(seed): 0.798 Vsfold4: 0.292 Sensitivity TurboFold(seed): 0.766 Vsfold4: 0.264 Positive Predictive Value TurboFold(seed): 0.835 Vsfold4: 0.334 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	233 MXScarna(seed) vs Vsfold4 Matthews Correlation Coefficient MXScarna(seed): 0.750 Vsfold4: 0.368 Sensitivity MXScarna(seed): 0.712 Vsfold4: 0.337 Positive Predictive Value MXScarna(seed): 0.793 Vsfold4: 0.409 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 CentroidAlifold(20) vs Vsfold4 Matthews Correlation Coefficient CentroidAlifold(20): 0.849 Vsfold4: 0.502 Sensitivity CentroidAlifold(20): 0.754 Vsfold4: 0.466 Positive Predictive Value CentroidAlifold(20): 0.957 Vsfold4: 0.546 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 PETfold_pre2.0(20) vs Vsfold4 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 Vsfold4: 0.502 Sensitivity PETfold_pre2.0(20): 0.737 Vsfold4: 0.466 Positive Predictive Value PETfold_pre2.0(20): 0.975 Vsfold4: 0.546 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 MXScarna(20) vs Vsfold4 Matthews Correlation Coefficient MXScarna(20): 0.838 Vsfold4: 0.502 Sensitivity MXScarna(20): 0.791 Vsfold4: 0.466 Positive Predictive Value MXScarna(20): 0.891 Vsfold4: 0.546 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	314 PPfold(20) vs Vsfold4 Matthews Correlation Coefficient PPfold(20): 0.839 Vsfold4: 0.511 Sensitivity PPfold(20): 0.721 Vsfold4: 0.475 Positive Predictive Value PPfold(20): 0.977 Vsfold4: 0.556 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RNAalifold(20) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(20): 0.816 Vsfold4: 0.502 Sensitivity RNAalifold(20): 0.690 Vsfold4: 0.466 Positive Predictive Value RNAalifold(20): 0.966 Vsfold4: 0.546 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RSpredict(20) vs Vsfold4 Matthews Correlation Coefficient RSpredict(20): 0.789 Vsfold4: 0.502 Sensitivity RSpredict(20): 0.693 Vsfold4: 0.466 Positive Predictive Value RSpredict(20): 0.901 Vsfold4: 0.546 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 IPknot vs Vsfold4 Matthews Correlation Coefficient IPknot: 0.694 Vsfold4: 0.487 Sensitivity IPknot: 0.661 Vsfold4: 0.447 Positive Predictive Value IPknot: 0.733 Vsfold4: 0.537 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	311 Multilign(20) vs Vsfold4 Matthews Correlation Coefficient Multilign(20): 0.784 Vsfold4: 0.509 Sensitivity Multilign(20): 0.697 Vsfold4: 0.473 Positive Predictive Value Multilign(20): 0.885 Vsfold4: 0.555 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 CentroidFold vs Vsfold4 Matthews Correlation Coefficient CentroidFold: 0.645 Vsfold4: 0.487 Sensitivity CentroidFold: 0.612 Vsfold4: 0.447 Positive Predictive Value CentroidFold: 0.684 Vsfold4: 0.537 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 Contrafold vs Vsfold4 Matthews Correlation Coefficient Contrafold: 0.643 Vsfold4: 0.487 Sensitivity Contrafold: 0.634 Vsfold4: 0.447 Positive Predictive Value Contrafold: 0.657 Vsfold4: 0.537 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	315 RNASampler(20) vs Vsfold4 Matthews Correlation Coefficient RNASampler(20): 0.770 Vsfold4: 0.505 Sensitivity RNASampler(20): 0.622 Vsfold4: 0.469 Positive Predictive Value RNASampler(20): 0.957 Vsfold4: 0.549 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	319 Murlet(20) vs Vsfold4 Matthews Correlation Coefficient Murlet(20): 0.750 Vsfold4: 0.503 Sensitivity Murlet(20): 0.619 Vsfold4: 0.467 Positive Predictive Value Murlet(20): 0.913 Vsfold4: 0.548 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 CMfinder(seed) vs Vsfold4 Matthews Correlation Coefficient CMfinder(seed): 0.571 Vsfold4: 0.403 Sensitivity CMfinder(seed): 0.439 Vsfold4: 0.355 Positive Predictive Value CMfinder(seed): 0.747 Vsfold4: 0.464 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 MaxExpect vs Vsfold4 Matthews Correlation Coefficient MaxExpect: 0.633 Vsfold4: 0.487 Sensitivity MaxExpect: 0.617 Vsfold4: 0.447 Positive Predictive Value MaxExpect: 0.654 Vsfold4: 0.537 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	316 CMfinder(20) vs Vsfold4 Matthews Correlation Coefficient CMfinder(20): 0.735 Vsfold4: 0.507 Sensitivity CMfinder(20): 0.603 Vsfold4: 0.472 Positive Predictive Value CMfinder(20): 0.899 Vsfold4: 0.551 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	881 CRWrnafold vs Vsfold4 Matthews Correlation Coefficient CRWrnafold: 0.630 Vsfold4: 0.487 Sensitivity CRWrnafold: 0.618 Vsfold4: 0.447 Positive Predictive Value CRWrnafold: 0.648 Vsfold4: 0.537 Number of pairs reference - predicted secondary structure: 881 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 ProbKnot vs Vsfold4 Matthews Correlation Coefficient ProbKnot: 0.630 Vsfold4: 0.487 Sensitivity ProbKnot: 0.622 Vsfold4: 0.447 Positive Predictive Value ProbKnot: 0.644 Vsfold4: 0.537 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 Mastr(20) vs Vsfold4 Matthews Correlation Coefficient Mastr(20): 0.708 Vsfold4: 0.502 Sensitivity Mastr(20): 0.635 Vsfold4: 0.466 Positive Predictive Value Mastr(20): 0.793 Vsfold4: 0.546 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 Fold vs Vsfold4 Matthews Correlation Coefficient Fold: 0.628 Vsfold4: 0.487 Sensitivity Fold: 0.620 Vsfold4: 0.447 Positive Predictive Value Fold: 0.641 Vsfold4: 0.537 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 UNAFold vs Vsfold4 Matthews Correlation Coefficient UNAFold: 0.620 Vsfold4: 0.487 Sensitivity UNAFold: 0.605 Vsfold4: 0.447 Positive Predictive Value UNAFold: 0.639 Vsfold4: 0.537 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 PknotsRG vs Vsfold4 Matthews Correlation Coefficient PknotsRG: 0.617 Vsfold4: 0.487 Sensitivity PknotsRG: 0.610 Vsfold4: 0.447 Positive Predictive Value PknotsRG: 0.630 Vsfold4: 0.537 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 Sfold vs Vsfold4 Matthews Correlation Coefficient Sfold: 0.618 Vsfold4: 0.487 Sensitivity Sfold: 0.581 Vsfold4: 0.447 Positive Predictive Value Sfold: 0.663 Vsfold4: 0.537 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	205 RNAalifold(seed) vs Vsfold4 Matthews Correlation Coefficient RNAalifold(seed): 0.610 Vsfold4: 0.338 Sensitivity RNAalifold(seed): 0.404 Vsfold4: 0.307 Positive Predictive Value RNAalifold(seed): 0.923 Vsfold4: 0.379 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 RNAsubopt vs Vsfold4 Matthews Correlation Coefficient RNAsubopt: 0.615 Vsfold4: 0.487 Sensitivity RNAsubopt: 0.609 Vsfold4: 0.447 Positive Predictive Value RNAsubopt: 0.626 Vsfold4: 0.537 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	875 HotKnots vs Vsfold4 Matthews Correlation Coefficient HotKnots: 0.613 Vsfold4: 0.487 Sensitivity HotKnots: 0.607 Vsfold4: 0.446 Positive Predictive Value HotKnots: 0.624 Vsfold4: 0.538 Number of pairs reference - predicted secondary structure: 875 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 RNAfold vs Vsfold4 Matthews Correlation Coefficient RNAfold: 0.612 Vsfold4: 0.487 Sensitivity RNAfold: 0.604 Vsfold4: 0.447 Positive Predictive Value RNAfold: 0.626 Vsfold4: 0.537 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 RNAshapes vs Vsfold4 Matthews Correlation Coefficient RNAshapes: 0.612 Vsfold4: 0.487 Sensitivity RNAshapes: 0.602 Vsfold4: 0.447 Positive Predictive Value RNAshapes: 0.628 Vsfold4: 0.537 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	86 RNASampler(seed) vs Vsfold4 Matthews Correlation Coefficient RNASampler(seed): 0.557 Vsfold4: 0.411 Sensitivity RNASampler(seed): 0.389 Vsfold4: 0.363 Positive Predictive Value RNASampler(seed): 0.802 Vsfold4: 0.472 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	530 Afold vs Vsfold4 Matthews Correlation Coefficient Afold: 0.558 Vsfold4: 0.402 Sensitivity Afold: 0.541 Vsfold4: 0.361 Positive Predictive Value Afold: 0.582 Vsfold4: 0.456 Number of pairs reference - predicted secondary structure: 530 Wilcoxon single-rank test P-value: 3.56938820447e-08	697 Pknots vs Vsfold4 Matthews Correlation Coefficient Pknots: 0.606 Vsfold4: 0.592 Sensitivity Pknots: 0.595 Vsfold4: 0.544 Positive Predictive Value Pknots: 0.624 Vsfold4: 0.651 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 McQFold vs Vsfold4 Matthews Correlation Coefficient McQFold: 0.583 Vsfold4: 0.487 Sensitivity McQFold: 0.557 Vsfold4: 0.447 Positive Predictive Value McQFold: 0.616 Vsfold4: 0.537 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 Carnac(20) vs Vsfold4 Matthews Correlation Coefficient Carnac(20): 0.675 Vsfold4: 0.502 Sensitivity Carnac(20): 0.500 Vsfold4: 0.466 Positive Predictive Value Carnac(20): 0.915 Vsfold4: 0.546 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 RNASLOpt vs Vsfold4 Matthews Correlation Coefficient RNASLOpt: 0.562 Vsfold4: 0.487 Sensitivity RNASLOpt: 0.521 Vsfold4: 0.447 Positive Predictive Value RNASLOpt: 0.613 Vsfold4: 0.537 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	796 Cylofold vs Vsfold4 Matthews Correlation Coefficient Cylofold: 0.577 Vsfold4: 0.515 Sensitivity Cylofold: 0.554 Vsfold4: 0.472 Positive Predictive Value Cylofold: 0.608 Vsfold4: 0.570 Number of pairs reference - predicted secondary structure: 796 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Multilign(seed) vs Vsfold4 Matthews Correlation Coefficient Multilign(seed): 0.485 Vsfold4: 0.332 Sensitivity Multilign(seed): 0.386 Vsfold4: 0.298 Positive Predictive Value Multilign(seed): 0.619 Vsfold4: 0.383 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.4651262096e-08	882 RNAwolf vs Vsfold4 Matthews Correlation Coefficient RNAwolf: 0.518 Vsfold4: 0.487 Sensitivity RNAwolf: 0.523 Vsfold4: 0.447 Positive Predictive Value RNAwolf: 0.520 Vsfold4: 0.537 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	40 PPfold(seed) vs Vsfold4 Matthews Correlation Coefficient PPfold(seed): 0.380 Vsfold4: 0.333 Sensitivity PPfold(seed): 0.170 Vsfold4: 0.305 Positive Predictive Value PPfold(seed): 0.852 Vsfold4: 0.372 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	91 Murlet(seed) vs Vsfold4 Matthews Correlation Coefficient Murlet(seed): 0.468 Vsfold4: 0.402 Sensitivity Murlet(seed): 0.266 Vsfold4: 0.357 Positive Predictive Value Murlet(seed): 0.828 Vsfold4: 0.461 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 Vsfold4 vs Alterna Matthews Correlation Coefficient Vsfold4: 0.596 Alterna: 0.552 Sensitivity Vsfold4: 0.547 Alterna: 0.547 Positive Predictive Value Vsfold4: 0.656 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	123 Carnac(seed) vs Vsfold4 Matthews Correlation Coefficient Carnac(seed): 0.415 Vsfold4: 0.379 Sensitivity Carnac(seed): 0.196 Vsfold4: 0.342 Positive Predictive Value Carnac(seed): 0.884 Vsfold4: 0.429 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08		- RSpredict(seed) vs Vsfold4 Matthews Correlation Coefficient RSpredict(seed): 0.373 Vsfold4: 0.355 Sensitivity RSpredict(seed): 0.251 Vsfold4: 0.324 Positive Predictive Value RSpredict(seed): 0.562 Vsfold4: 0.397 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 4.83792096436e-08	+ Vsfold4 vs Vsfold5 Matthews Correlation Coefficient Vsfold4: 0.487 Vsfold5: 0.477 Sensitivity Vsfold4: 0.447 Vsfold5: 0.450 Positive Predictive Value Vsfold4: 0.537 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs RDfolder Matthews Correlation Coefficient Vsfold4: 0.596 RDfolder: 0.520 Sensitivity Vsfold4: 0.547 RDfolder: 0.464 Positive Predictive Value Vsfold4: 0.656 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs MCFold Matthews Correlation Coefficient Vsfold4: 0.500 MCFold: 0.473 Sensitivity Vsfold4: 0.456 MCFold: 0.524 Positive Predictive Value Vsfold4: 0.555 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs NanoFolder Matthews Correlation Coefficient Vsfold4: 0.436 NanoFolder: 0.335 Sensitivity Vsfold4: 0.399 NanoFolder: 0.384 Positive Predictive Value Vsfold4: 0.485 NanoFolder: 0.301 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold4 vs Mastr(seed) Matthews Correlation Coefficient Vsfold4: 0.368 Mastr(seed): 0.263 Sensitivity Vsfold4: 0.337 Mastr(seed): 0.089 Positive Predictive Value Vsfold4: 0.410 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08
RSpredict(seed)	216 ContextFold vs RSpredict(seed) Matthews Correlation Coefficient ContextFold: 0.839 RSpredict(seed): 0.373 Sensitivity ContextFold: 0.812 RSpredict(seed): 0.251 Positive Predictive Value ContextFold: 0.868 RSpredict(seed): 0.562 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	141 TurboFold(20) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(20): 0.830 RSpredict(seed): 0.414 Sensitivity TurboFold(20): 0.812 RSpredict(seed): 0.279 Positive Predictive Value TurboFold(20): 0.850 RSpredict(seed): 0.622 Number of pairs reference - predicted secondary structure: 141 Wilcoxon single-rank test P-value: 3.56938820447e-08	216 CentroidAlifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.790 RSpredict(seed): 0.373 Sensitivity CentroidAlifold(seed): 0.699 RSpredict(seed): 0.251 Positive Predictive Value CentroidAlifold(seed): 0.896 RSpredict(seed): 0.562 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	216 CentroidHomfold‑LAST vs RSpredict(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.794 RSpredict(seed): 0.373 Sensitivity CentroidHomfold‑LAST: 0.737 RSpredict(seed): 0.251 Positive Predictive Value CentroidHomfold‑LAST: 0.858 RSpredict(seed): 0.562 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	213 PETfold_pre2.0(seed) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.750 RSpredict(seed): 0.367 Sensitivity PETfold_pre2.0(seed): 0.654 RSpredict(seed): 0.245 Positive Predictive Value PETfold_pre2.0(seed): 0.862 RSpredict(seed): 0.557 Number of pairs reference - predicted secondary structure: 213 Wilcoxon single-rank test P-value: 3.56938820447e-08	32 TurboFold(seed) vs RSpredict(seed) Matthews Correlation Coefficient TurboFold(seed): 0.790 RSpredict(seed): 0.462 Sensitivity TurboFold(seed): 0.759 RSpredict(seed): 0.355 Positive Predictive Value TurboFold(seed): 0.826 RSpredict(seed): 0.608 Number of pairs reference - predicted secondary structure: 32 Wilcoxon single-rank test P-value: 3.56938820447e-08	216 MXScarna(seed) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(seed): 0.739 RSpredict(seed): 0.373 Sensitivity MXScarna(seed): 0.701 RSpredict(seed): 0.251 Positive Predictive Value MXScarna(seed): 0.783 RSpredict(seed): 0.562 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	141 CentroidAlifold(20) vs RSpredict(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.702 RSpredict(seed): 0.414 Sensitivity CentroidAlifold(20): 0.525 RSpredict(seed): 0.279 Positive Predictive Value CentroidAlifold(20): 0.944 RSpredict(seed): 0.622 Number of pairs reference - predicted secondary structure: 141 Wilcoxon single-rank test P-value: 3.56938820447e-08	141 PETfold_pre2.0(20) vs RSpredict(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.641 RSpredict(seed): 0.414 Sensitivity PETfold_pre2.0(20): 0.440 RSpredict(seed): 0.279 Positive Predictive Value PETfold_pre2.0(20): 0.938 RSpredict(seed): 0.622 Number of pairs reference - predicted secondary structure: 141 Wilcoxon single-rank test P-value: 3.56938820447e-08	141 MXScarna(20) vs RSpredict(seed) Matthews Correlation Coefficient MXScarna(20): 0.764 RSpredict(seed): 0.414 Sensitivity MXScarna(20): 0.686 RSpredict(seed): 0.279 Positive Predictive Value MXScarna(20): 0.854 RSpredict(seed): 0.622 Number of pairs reference - predicted secondary structure: 141 Wilcoxon single-rank test P-value: 3.56938820447e-08	135 PPfold(20) vs RSpredict(seed) Matthews Correlation Coefficient PPfold(20): 0.625 RSpredict(seed): 0.425 Sensitivity PPfold(20): 0.415 RSpredict(seed): 0.289 Positive Predictive Value PPfold(20): 0.944 RSpredict(seed): 0.633 Number of pairs reference - predicted secondary structure: 135 Wilcoxon single-rank test P-value: 3.56938820447e-08	141 RNAalifold(20) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(20): 0.642 RSpredict(seed): 0.414 Sensitivity RNAalifold(20): 0.442 RSpredict(seed): 0.279 Positive Predictive Value RNAalifold(20): 0.937 RSpredict(seed): 0.622 Number of pairs reference - predicted secondary structure: 141 Wilcoxon single-rank test P-value: 3.56938820447e-08	141 RSpredict(20) vs RSpredict(seed) Matthews Correlation Coefficient RSpredict(20): 0.716 RSpredict(seed): 0.414 Sensitivity RSpredict(20): 0.594 RSpredict(seed): 0.279 Positive Predictive Value RSpredict(20): 0.866 RSpredict(seed): 0.622 Number of pairs reference - predicted secondary structure: 141 Wilcoxon single-rank test P-value: 3.56938820447e-08	216 IPknot vs RSpredict(seed) Matthews Correlation Coefficient IPknot: 0.733 RSpredict(seed): 0.373 Sensitivity IPknot: 0.708 RSpredict(seed): 0.251 Positive Predictive Value IPknot: 0.762 RSpredict(seed): 0.562 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	132 Multilign(20) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(20): 0.593 RSpredict(seed): 0.436 Sensitivity Multilign(20): 0.447 RSpredict(seed): 0.298 Positive Predictive Value Multilign(20): 0.793 RSpredict(seed): 0.645 Number of pairs reference - predicted secondary structure: 132 Wilcoxon single-rank test P-value: 3.56938820447e-08	216 CentroidFold vs RSpredict(seed) Matthews Correlation Coefficient CentroidFold: 0.699 RSpredict(seed): 0.373 Sensitivity CentroidFold: 0.665 RSpredict(seed): 0.251 Positive Predictive Value CentroidFold: 0.739 RSpredict(seed): 0.562 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	216 Contrafold vs RSpredict(seed) Matthews Correlation Coefficient Contrafold: 0.692 RSpredict(seed): 0.373 Sensitivity Contrafold: 0.681 RSpredict(seed): 0.251 Positive Predictive Value Contrafold: 0.707 RSpredict(seed): 0.562 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	137 RNASampler(20) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(20): 0.604 RSpredict(seed): 0.417 Sensitivity RNASampler(20): 0.394 RSpredict(seed): 0.282 Positive Predictive Value RNASampler(20): 0.931 RSpredict(seed): 0.626 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 3.56938820447e-08	140 Murlet(20) vs RSpredict(seed) Matthews Correlation Coefficient Murlet(20): 0.609 RSpredict(seed): 0.412 Sensitivity Murlet(20): 0.404 RSpredict(seed): 0.276 Positive Predictive Value Murlet(20): 0.922 RSpredict(seed): 0.621 Number of pairs reference - predicted secondary structure: 140 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 CMfinder(seed) vs RSpredict(seed) Matthews Correlation Coefficient CMfinder(seed): 0.571 RSpredict(seed): 0.512 Sensitivity CMfinder(seed): 0.439 RSpredict(seed): 0.408 Positive Predictive Value CMfinder(seed): 0.747 RSpredict(seed): 0.649 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	216 MaxExpect vs RSpredict(seed) Matthews Correlation Coefficient MaxExpect: 0.694 RSpredict(seed): 0.373 Sensitivity MaxExpect: 0.684 RSpredict(seed): 0.251 Positive Predictive Value MaxExpect: 0.707 RSpredict(seed): 0.562 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	137 CMfinder(20) vs RSpredict(seed) Matthews Correlation Coefficient CMfinder(20): 0.649 RSpredict(seed): 0.427 Sensitivity CMfinder(20): 0.500 RSpredict(seed): 0.290 Positive Predictive Value CMfinder(20): 0.846 RSpredict(seed): 0.636 Number of pairs reference - predicted secondary structure: 137 Wilcoxon single-rank test P-value: 3.56938820447e-08	216 CRWrnafold vs RSpredict(seed) Matthews Correlation Coefficient CRWrnafold: 0.705 RSpredict(seed): 0.373 Sensitivity CRWrnafold: 0.696 RSpredict(seed): 0.251 Positive Predictive Value CRWrnafold: 0.716 RSpredict(seed): 0.562 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	216 ProbKnot vs RSpredict(seed) Matthews Correlation Coefficient ProbKnot: 0.687 RSpredict(seed): 0.373 Sensitivity ProbKnot: 0.680 RSpredict(seed): 0.251 Positive Predictive Value ProbKnot: 0.697 RSpredict(seed): 0.562 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	141 Mastr(20) vs RSpredict(seed) Matthews Correlation Coefficient Mastr(20): 0.659 RSpredict(seed): 0.414 Sensitivity Mastr(20): 0.520 RSpredict(seed): 0.279 Positive Predictive Value Mastr(20): 0.839 RSpredict(seed): 0.622 Number of pairs reference - predicted secondary structure: 141 Wilcoxon single-rank test P-value: 3.56938820447e-08	216 Fold vs RSpredict(seed) Matthews Correlation Coefficient Fold: 0.701 RSpredict(seed): 0.373 Sensitivity Fold: 0.699 RSpredict(seed): 0.251 Positive Predictive Value Fold: 0.706 RSpredict(seed): 0.562 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	216 UNAFold vs RSpredict(seed) Matthews Correlation Coefficient UNAFold: 0.702 RSpredict(seed): 0.373 Sensitivity UNAFold: 0.695 RSpredict(seed): 0.251 Positive Predictive Value UNAFold: 0.713 RSpredict(seed): 0.562 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	216 PknotsRG vs RSpredict(seed) Matthews Correlation Coefficient PknotsRG: 0.705 RSpredict(seed): 0.373 Sensitivity PknotsRG: 0.705 RSpredict(seed): 0.251 Positive Predictive Value PknotsRG: 0.710 RSpredict(seed): 0.562 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	216 Sfold vs RSpredict(seed) Matthews Correlation Coefficient Sfold: 0.686 RSpredict(seed): 0.373 Sensitivity Sfold: 0.656 RSpredict(seed): 0.251 Positive Predictive Value Sfold: 0.721 RSpredict(seed): 0.562 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	205 RNAalifold(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.610 RSpredict(seed): 0.385 Sensitivity RNAalifold(seed): 0.404 RSpredict(seed): 0.262 Positive Predictive Value RNAalifold(seed): 0.923 RSpredict(seed): 0.571 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	216 RNAsubopt vs RSpredict(seed) Matthews Correlation Coefficient RNAsubopt: 0.655 RSpredict(seed): 0.373 Sensitivity RNAsubopt: 0.654 RSpredict(seed): 0.251 Positive Predictive Value RNAsubopt: 0.660 RSpredict(seed): 0.562 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	212 HotKnots vs RSpredict(seed) Matthews Correlation Coefficient HotKnots: 0.688 RSpredict(seed): 0.381 Sensitivity HotKnots: 0.689 RSpredict(seed): 0.258 Positive Predictive Value HotKnots: 0.691 RSpredict(seed): 0.570 Number of pairs reference - predicted secondary structure: 212 Wilcoxon single-rank test P-value: 3.56938820447e-08	216 RNAfold vs RSpredict(seed) Matthews Correlation Coefficient RNAfold: 0.694 RSpredict(seed): 0.373 Sensitivity RNAfold: 0.691 RSpredict(seed): 0.251 Positive Predictive Value RNAfold: 0.702 RSpredict(seed): 0.562 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	216 RNAshapes vs RSpredict(seed) Matthews Correlation Coefficient RNAshapes: 0.680 RSpredict(seed): 0.373 Sensitivity RNAshapes: 0.677 RSpredict(seed): 0.251 Positive Predictive Value RNAshapes: 0.686 RSpredict(seed): 0.562 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	86 RNASampler(seed) vs RSpredict(seed) Matthews Correlation Coefficient RNASampler(seed): 0.557 RSpredict(seed): 0.511 Sensitivity RNASampler(seed): 0.389 RSpredict(seed): 0.405 Positive Predictive Value RNASampler(seed): 0.802 RSpredict(seed): 0.651 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	162 Afold vs RSpredict(seed) Matthews Correlation Coefficient Afold: 0.649 RSpredict(seed): 0.405 Sensitivity Afold: 0.646 RSpredict(seed): 0.283 Positive Predictive Value Afold: 0.657 RSpredict(seed): 0.586 Number of pairs reference - predicted secondary structure: 162 Wilcoxon single-rank test P-value: 3.56938820447e-08	146 Pknots vs RSpredict(seed) Matthews Correlation Coefficient Pknots: 0.509 RSpredict(seed): 0.475 Sensitivity Pknots: 0.504 RSpredict(seed): 0.341 Positive Predictive Value Pknots: 0.523 RSpredict(seed): 0.669 Number of pairs reference - predicted secondary structure: 146 Wilcoxon single-rank test P-value: 3.56938820447e-08	216 McQFold vs RSpredict(seed) Matthews Correlation Coefficient McQFold: 0.562 RSpredict(seed): 0.373 Sensitivity McQFold: 0.537 RSpredict(seed): 0.251 Positive Predictive Value McQFold: 0.593 RSpredict(seed): 0.562 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	141 Carnac(20) vs RSpredict(seed) Matthews Correlation Coefficient Carnac(20): 0.467 RSpredict(seed): 0.414 Sensitivity Carnac(20): 0.260 RSpredict(seed): 0.279 Positive Predictive Value Carnac(20): 0.845 RSpredict(seed): 0.622 Number of pairs reference - predicted secondary structure: 141 Wilcoxon single-rank test P-value: 3.56938820447e-08	216 RNASLOpt vs RSpredict(seed) Matthews Correlation Coefficient RNASLOpt: 0.579 RSpredict(seed): 0.373 Sensitivity RNASLOpt: 0.530 RSpredict(seed): 0.251 Positive Predictive Value RNASLOpt: 0.638 RSpredict(seed): 0.562 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	197 Cylofold vs RSpredict(seed) Matthews Correlation Coefficient Cylofold: 0.518 RSpredict(seed): 0.402 Sensitivity Cylofold: 0.491 RSpredict(seed): 0.279 Positive Predictive Value Cylofold: 0.552 RSpredict(seed): 0.588 Number of pairs reference - predicted secondary structure: 197 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Multilign(seed) vs RSpredict(seed) Matthews Correlation Coefficient Multilign(seed): 0.485 RSpredict(seed): 0.479 Sensitivity Multilign(seed): 0.386 RSpredict(seed): 0.423 Positive Predictive Value Multilign(seed): 0.619 RSpredict(seed): 0.552 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 0.0114155930811	216 RNAwolf vs RSpredict(seed) Matthews Correlation Coefficient RNAwolf: 0.529 RSpredict(seed): 0.373 Sensitivity RNAwolf: 0.534 RSpredict(seed): 0.251 Positive Predictive Value RNAwolf: 0.529 RSpredict(seed): 0.562 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	40 PPfold(seed) vs RSpredict(seed) Matthews Correlation Coefficient PPfold(seed): 0.380 RSpredict(seed): 0.375 Sensitivity PPfold(seed): 0.170 RSpredict(seed): 0.254 Positive Predictive Value PPfold(seed): 0.852 RSpredict(seed): 0.563 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 0.00476252034473	91 RSpredict(seed) vs Murlet(seed) Matthews Correlation Coefficient RSpredict(seed): 0.491 Murlet(seed): 0.468 Sensitivity RSpredict(seed): 0.380 Murlet(seed): 0.266 Positive Predictive Value RSpredict(seed): 0.641 Murlet(seed): 0.828 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	145 Alterna vs RSpredict(seed) Matthews Correlation Coefficient Alterna: 0.558 RSpredict(seed): 0.472 Sensitivity Alterna: 0.548 RSpredict(seed): 0.337 Positive Predictive Value Alterna: 0.575 RSpredict(seed): 0.669 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	120 RSpredict(seed) vs Carnac(seed) Matthews Correlation Coefficient RSpredict(seed): 0.439 Carnac(seed): 0.424 Sensitivity RSpredict(seed): 0.318 Carnac(seed): 0.205 Positive Predictive Value RSpredict(seed): 0.611 Carnac(seed): 0.884 Number of pairs reference - predicted secondary structure: 120 Wilcoxon single-rank test P-value: 1.70738736246e-07	216 RSpredict(seed) vs Vsfold4 Matthews Correlation Coefficient RSpredict(seed): 0.373 Vsfold4: 0.355 Sensitivity RSpredict(seed): 0.251 Vsfold4: 0.324 Positive Predictive Value RSpredict(seed): 0.562 Vsfold4: 0.397 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 4.83792096436e-08		+ RSpredict(seed) vs Vsfold5 Matthews Correlation Coefficient RSpredict(seed): 0.373 Vsfold5: 0.309 Sensitivity RSpredict(seed): 0.251 Vsfold5: 0.289 Positive Predictive Value RSpredict(seed): 0.562 Vsfold5: 0.338 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	= RSpredict(seed) vs RDfolder Matthews Correlation Coefficient RSpredict(seed): 0.472 RDfolder: 0.468 Sensitivity RSpredict(seed): 0.337 RDfolder: 0.402 Positive Predictive Value RSpredict(seed): 0.669 RDfolder: 0.552 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 0.0215355173778	- MCFold vs RSpredict(seed) Matthews Correlation Coefficient MCFold: 0.472 RSpredict(seed): 0.391 Sensitivity MCFold: 0.523 RSpredict(seed): 0.265 Positive Predictive Value MCFold: 0.432 RSpredict(seed): 0.583 Number of pairs reference - predicted secondary structure: 185 Wilcoxon single-rank test P-value: 3.56938820447e-08	- NanoFolder vs RSpredict(seed) Matthews Correlation Coefficient NanoFolder: 0.391 RSpredict(seed): 0.338 Sensitivity NanoFolder: 0.446 RSpredict(seed): 0.215 Positive Predictive Value NanoFolder: 0.350 RSpredict(seed): 0.539 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RSpredict(seed) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(seed): 0.373 Mastr(seed): 0.276 Sensitivity RSpredict(seed): 0.251 Mastr(seed): 0.097 Positive Predictive Value RSpredict(seed): 0.562 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08
Vsfold5	882 ContextFold vs Vsfold5 Matthews Correlation Coefficient ContextFold: 0.779 Vsfold5: 0.477 Sensitivity ContextFold: 0.741 Vsfold5: 0.450 Positive Predictive Value ContextFold: 0.823 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 TurboFold(20) vs Vsfold5 Matthews Correlation Coefficient TurboFold(20): 0.889 Vsfold5: 0.457 Sensitivity TurboFold(20): 0.861 Vsfold5: 0.437 Positive Predictive Value TurboFold(20): 0.919 Vsfold5: 0.484 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	216 CentroidAlifold(seed) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(seed): 0.790 Vsfold5: 0.309 Sensitivity CentroidAlifold(seed): 0.699 Vsfold5: 0.289 Positive Predictive Value CentroidAlifold(seed): 0.896 Vsfold5: 0.338 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 CentroidHomfold‑LAST vs Vsfold5 Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.736 Vsfold5: 0.477 Sensitivity CentroidHomfold‑LAST: 0.665 Vsfold5: 0.450 Positive Predictive Value CentroidHomfold‑LAST: 0.818 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	498 PETfold_pre2.0(seed) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.879 Vsfold5: 0.489 Sensitivity PETfold_pre2.0(seed): 0.825 Vsfold5: 0.472 Positive Predictive Value PETfold_pre2.0(seed): 0.938 Vsfold5: 0.514 Number of pairs reference - predicted secondary structure: 498 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 TurboFold(seed) vs Vsfold5 Matthews Correlation Coefficient TurboFold(seed): 0.798 Vsfold5: 0.295 Sensitivity TurboFold(seed): 0.766 Vsfold5: 0.266 Positive Predictive Value TurboFold(seed): 0.835 Vsfold5: 0.337 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	233 MXScarna(seed) vs Vsfold5 Matthews Correlation Coefficient MXScarna(seed): 0.750 Vsfold5: 0.328 Sensitivity MXScarna(seed): 0.712 Vsfold5: 0.309 Positive Predictive Value MXScarna(seed): 0.793 Vsfold5: 0.356 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 CentroidAlifold(20) vs Vsfold5 Matthews Correlation Coefficient CentroidAlifold(20): 0.849 Vsfold5: 0.457 Sensitivity CentroidAlifold(20): 0.754 Vsfold5: 0.437 Positive Predictive Value CentroidAlifold(20): 0.957 Vsfold5: 0.484 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 PETfold_pre2.0(20) vs Vsfold5 Matthews Correlation Coefficient PETfold_pre2.0(20): 0.847 Vsfold5: 0.457 Sensitivity PETfold_pre2.0(20): 0.737 Vsfold5: 0.437 Positive Predictive Value PETfold_pre2.0(20): 0.975 Vsfold5: 0.484 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 MXScarna(20) vs Vsfold5 Matthews Correlation Coefficient MXScarna(20): 0.838 Vsfold5: 0.457 Sensitivity MXScarna(20): 0.791 Vsfold5: 0.437 Positive Predictive Value MXScarna(20): 0.891 Vsfold5: 0.484 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	314 PPfold(20) vs Vsfold5 Matthews Correlation Coefficient PPfold(20): 0.839 Vsfold5: 0.465 Sensitivity PPfold(20): 0.721 Vsfold5: 0.445 Positive Predictive Value PPfold(20): 0.977 Vsfold5: 0.492 Number of pairs reference - predicted secondary structure: 314 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RNAalifold(20) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(20): 0.816 Vsfold5: 0.457 Sensitivity RNAalifold(20): 0.690 Vsfold5: 0.437 Positive Predictive Value RNAalifold(20): 0.966 Vsfold5: 0.484 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 RSpredict(20) vs Vsfold5 Matthews Correlation Coefficient RSpredict(20): 0.789 Vsfold5: 0.457 Sensitivity RSpredict(20): 0.693 Vsfold5: 0.437 Positive Predictive Value RSpredict(20): 0.901 Vsfold5: 0.484 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 IPknot vs Vsfold5 Matthews Correlation Coefficient IPknot: 0.694 Vsfold5: 0.477 Sensitivity IPknot: 0.661 Vsfold5: 0.450 Positive Predictive Value IPknot: 0.733 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	311 Multilign(20) vs Vsfold5 Matthews Correlation Coefficient Multilign(20): 0.784 Vsfold5: 0.469 Sensitivity Multilign(20): 0.697 Vsfold5: 0.449 Positive Predictive Value Multilign(20): 0.885 Vsfold5: 0.496 Number of pairs reference - predicted secondary structure: 311 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 CentroidFold vs Vsfold5 Matthews Correlation Coefficient CentroidFold: 0.645 Vsfold5: 0.477 Sensitivity CentroidFold: 0.612 Vsfold5: 0.450 Positive Predictive Value CentroidFold: 0.684 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 Contrafold vs Vsfold5 Matthews Correlation Coefficient Contrafold: 0.643 Vsfold5: 0.477 Sensitivity Contrafold: 0.634 Vsfold5: 0.450 Positive Predictive Value Contrafold: 0.657 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	315 RNASampler(20) vs Vsfold5 Matthews Correlation Coefficient RNASampler(20): 0.770 Vsfold5: 0.462 Sensitivity RNASampler(20): 0.622 Vsfold5: 0.442 Positive Predictive Value RNASampler(20): 0.957 Vsfold5: 0.489 Number of pairs reference - predicted secondary structure: 315 Wilcoxon single-rank test P-value: 3.56938820447e-08	319 Murlet(20) vs Vsfold5 Matthews Correlation Coefficient Murlet(20): 0.750 Vsfold5: 0.458 Sensitivity Murlet(20): 0.619 Vsfold5: 0.438 Positive Predictive Value Murlet(20): 0.913 Vsfold5: 0.485 Number of pairs reference - predicted secondary structure: 319 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 CMfinder(seed) vs Vsfold5 Matthews Correlation Coefficient CMfinder(seed): 0.571 Vsfold5: 0.383 Sensitivity CMfinder(seed): 0.439 Vsfold5: 0.348 Positive Predictive Value CMfinder(seed): 0.747 Vsfold5: 0.428 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 MaxExpect vs Vsfold5 Matthews Correlation Coefficient MaxExpect: 0.633 Vsfold5: 0.477 Sensitivity MaxExpect: 0.617 Vsfold5: 0.450 Positive Predictive Value MaxExpect: 0.654 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	316 CMfinder(20) vs Vsfold5 Matthews Correlation Coefficient CMfinder(20): 0.735 Vsfold5: 0.462 Sensitivity CMfinder(20): 0.603 Vsfold5: 0.443 Positive Predictive Value CMfinder(20): 0.899 Vsfold5: 0.489 Number of pairs reference - predicted secondary structure: 316 Wilcoxon single-rank test P-value: 3.56938820447e-08	881 CRWrnafold vs Vsfold5 Matthews Correlation Coefficient CRWrnafold: 0.630 Vsfold5: 0.477 Sensitivity CRWrnafold: 0.618 Vsfold5: 0.451 Positive Predictive Value CRWrnafold: 0.648 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 881 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 ProbKnot vs Vsfold5 Matthews Correlation Coefficient ProbKnot: 0.630 Vsfold5: 0.477 Sensitivity ProbKnot: 0.622 Vsfold5: 0.450 Positive Predictive Value ProbKnot: 0.644 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 Mastr(20) vs Vsfold5 Matthews Correlation Coefficient Mastr(20): 0.708 Vsfold5: 0.457 Sensitivity Mastr(20): 0.635 Vsfold5: 0.437 Positive Predictive Value Mastr(20): 0.793 Vsfold5: 0.484 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 Fold vs Vsfold5 Matthews Correlation Coefficient Fold: 0.628 Vsfold5: 0.477 Sensitivity Fold: 0.620 Vsfold5: 0.450 Positive Predictive Value Fold: 0.641 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 UNAFold vs Vsfold5 Matthews Correlation Coefficient UNAFold: 0.620 Vsfold5: 0.477 Sensitivity UNAFold: 0.605 Vsfold5: 0.450 Positive Predictive Value UNAFold: 0.639 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 PknotsRG vs Vsfold5 Matthews Correlation Coefficient PknotsRG: 0.617 Vsfold5: 0.477 Sensitivity PknotsRG: 0.610 Vsfold5: 0.450 Positive Predictive Value PknotsRG: 0.630 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 Sfold vs Vsfold5 Matthews Correlation Coefficient Sfold: 0.618 Vsfold5: 0.477 Sensitivity Sfold: 0.581 Vsfold5: 0.450 Positive Predictive Value Sfold: 0.663 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	205 RNAalifold(seed) vs Vsfold5 Matthews Correlation Coefficient RNAalifold(seed): 0.610 Vsfold5: 0.291 Sensitivity RNAalifold(seed): 0.404 Vsfold5: 0.271 Positive Predictive Value RNAalifold(seed): 0.923 Vsfold5: 0.321 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 RNAsubopt vs Vsfold5 Matthews Correlation Coefficient RNAsubopt: 0.615 Vsfold5: 0.477 Sensitivity RNAsubopt: 0.609 Vsfold5: 0.450 Positive Predictive Value RNAsubopt: 0.626 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	875 HotKnots vs Vsfold5 Matthews Correlation Coefficient HotKnots: 0.613 Vsfold5: 0.477 Sensitivity HotKnots: 0.607 Vsfold5: 0.451 Positive Predictive Value HotKnots: 0.624 Vsfold5: 0.513 Number of pairs reference - predicted secondary structure: 875 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 RNAfold vs Vsfold5 Matthews Correlation Coefficient RNAfold: 0.612 Vsfold5: 0.477 Sensitivity RNAfold: 0.604 Vsfold5: 0.450 Positive Predictive Value RNAfold: 0.626 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 RNAshapes vs Vsfold5 Matthews Correlation Coefficient RNAshapes: 0.612 Vsfold5: 0.477 Sensitivity RNAshapes: 0.602 Vsfold5: 0.450 Positive Predictive Value RNAshapes: 0.628 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	86 RNASampler(seed) vs Vsfold5 Matthews Correlation Coefficient RNASampler(seed): 0.557 Vsfold5: 0.390 Sensitivity RNASampler(seed): 0.389 Vsfold5: 0.356 Positive Predictive Value RNASampler(seed): 0.802 Vsfold5: 0.434 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	530 Afold vs Vsfold5 Matthews Correlation Coefficient Afold: 0.558 Vsfold5: 0.403 Sensitivity Afold: 0.541 Vsfold5: 0.370 Positive Predictive Value Afold: 0.582 Vsfold5: 0.447 Number of pairs reference - predicted secondary structure: 530 Wilcoxon single-rank test P-value: 3.56938820447e-08	697 Pknots vs Vsfold5 Matthews Correlation Coefficient Pknots: 0.606 Vsfold5: 0.579 Sensitivity Pknots: 0.595 Vsfold5: 0.548 Positive Predictive Value Pknots: 0.624 Vsfold5: 0.620 Number of pairs reference - predicted secondary structure: 697 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 McQFold vs Vsfold5 Matthews Correlation Coefficient McQFold: 0.583 Vsfold5: 0.477 Sensitivity McQFold: 0.557 Vsfold5: 0.450 Positive Predictive Value McQFold: 0.616 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	320 Carnac(20) vs Vsfold5 Matthews Correlation Coefficient Carnac(20): 0.675 Vsfold5: 0.457 Sensitivity Carnac(20): 0.500 Vsfold5: 0.437 Positive Predictive Value Carnac(20): 0.915 Vsfold5: 0.484 Number of pairs reference - predicted secondary structure: 320 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 RNASLOpt vs Vsfold5 Matthews Correlation Coefficient RNASLOpt: 0.562 Vsfold5: 0.477 Sensitivity RNASLOpt: 0.521 Vsfold5: 0.450 Positive Predictive Value RNASLOpt: 0.613 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	796 Cylofold vs Vsfold5 Matthews Correlation Coefficient Cylofold: 0.577 Vsfold5: 0.498 Sensitivity Cylofold: 0.554 Vsfold5: 0.469 Positive Predictive Value Cylofold: 0.608 Vsfold5: 0.536 Number of pairs reference - predicted secondary structure: 796 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Multilign(seed) vs Vsfold5 Matthews Correlation Coefficient Multilign(seed): 0.485 Vsfold5: 0.418 Sensitivity Multilign(seed): 0.386 Vsfold5: 0.386 Positive Predictive Value Multilign(seed): 0.619 Vsfold5: 0.464 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 1.93248927742e-08	882 RNAwolf vs Vsfold5 Matthews Correlation Coefficient RNAwolf: 0.518 Vsfold5: 0.477 Sensitivity RNAwolf: 0.523 Vsfold5: 0.450 Positive Predictive Value RNAwolf: 0.520 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	40 PPfold(seed) vs Vsfold5 Matthews Correlation Coefficient PPfold(seed): 0.380 Vsfold5: 0.316 Sensitivity PPfold(seed): 0.170 Vsfold5: 0.290 Positive Predictive Value PPfold(seed): 0.852 Vsfold5: 0.354 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	91 Murlet(seed) vs Vsfold5 Matthews Correlation Coefficient Murlet(seed): 0.468 Vsfold5: 0.363 Sensitivity Murlet(seed): 0.266 Vsfold5: 0.328 Positive Predictive Value Murlet(seed): 0.828 Vsfold5: 0.409 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 Vsfold5 vs Alterna Matthews Correlation Coefficient Vsfold5: 0.582 Alterna: 0.552 Sensitivity Vsfold5: 0.551 Alterna: 0.547 Positive Predictive Value Vsfold5: 0.623 Alterna: 0.566 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	123 Carnac(seed) vs Vsfold5 Matthews Correlation Coefficient Carnac(seed): 0.415 Vsfold5: 0.353 Sensitivity Carnac(seed): 0.196 Vsfold5: 0.325 Positive Predictive Value Carnac(seed): 0.884 Vsfold5: 0.392 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	882 Vsfold4 vs Vsfold5 Matthews Correlation Coefficient Vsfold4: 0.487 Vsfold5: 0.477 Sensitivity Vsfold4: 0.447 Vsfold5: 0.450 Positive Predictive Value Vsfold4: 0.537 Vsfold5: 0.512 Number of pairs reference - predicted secondary structure: 882 Wilcoxon single-rank test P-value: 3.56938820447e-08	216 RSpredict(seed) vs Vsfold5 Matthews Correlation Coefficient RSpredict(seed): 0.373 Vsfold5: 0.309 Sensitivity RSpredict(seed): 0.251 Vsfold5: 0.289 Positive Predictive Value RSpredict(seed): 0.562 Vsfold5: 0.338 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ Vsfold5 vs RDfolder Matthews Correlation Coefficient Vsfold5: 0.582 RDfolder: 0.520 Sensitivity Vsfold5: 0.551 RDfolder: 0.464 Positive Predictive Value Vsfold5: 0.623 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs MCFold Matthews Correlation Coefficient Vsfold5: 0.489 MCFold: 0.473 Sensitivity Vsfold5: 0.460 MCFold: 0.524 Positive Predictive Value Vsfold5: 0.527 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs NanoFolder Matthews Correlation Coefficient Vsfold5: 0.417 NanoFolder: 0.335 Sensitivity Vsfold5: 0.389 NanoFolder: 0.384 Positive Predictive Value Vsfold5: 0.455 NanoFolder: 0.301 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ Vsfold5 vs Mastr(seed) Matthews Correlation Coefficient Vsfold5: 0.328 Mastr(seed): 0.263 Sensitivity Vsfold5: 0.310 Mastr(seed): 0.089 Positive Predictive Value Vsfold5: 0.356 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08
RDfolder	693 ContextFold vs RDfolder Matthews Correlation Coefficient ContextFold: 0.765 RDfolder: 0.520 Sensitivity ContextFold: 0.723 RDfolder: 0.464 Positive Predictive Value ContextFold: 0.814 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	211 TurboFold(20) vs RDfolder Matthews Correlation Coefficient TurboFold(20): 0.913 RDfolder: 0.556 Sensitivity TurboFold(20): 0.887 RDfolder: 0.511 Positive Predictive Value TurboFold(20): 0.940 RDfolder: 0.611 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	145 CentroidAlifold(seed) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.781 RDfolder: 0.468 Sensitivity CentroidAlifold(seed): 0.674 RDfolder: 0.402 Positive Predictive Value CentroidAlifold(seed): 0.908 RDfolder: 0.552 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 CentroidHomfold‑LAST vs RDfolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.748 RDfolder: 0.520 Sensitivity CentroidHomfold‑LAST: 0.687 RDfolder: 0.464 Positive Predictive Value CentroidHomfold‑LAST: 0.818 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	360 PETfold_pre2.0(seed) vs RDfolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.909 RDfolder: 0.557 Sensitivity PETfold_pre2.0(seed): 0.870 RDfolder: 0.511 Positive Predictive Value PETfold_pre2.0(seed): 0.950 RDfolder: 0.615 Number of pairs reference - predicted secondary structure: 360 Wilcoxon single-rank test P-value: 3.56938820447e-08	24 TurboFold(seed) vs RDfolder Matthews Correlation Coefficient TurboFold(seed): 0.720 RDfolder: 0.512 Sensitivity TurboFold(seed): 0.663 RDfolder: 0.453 Positive Predictive Value TurboFold(seed): 0.786 RDfolder: 0.588 Number of pairs reference - predicted secondary structure: 24 Wilcoxon single-rank test P-value: 5.10776592382e-08	156 MXScarna(seed) vs RDfolder Matthews Correlation Coefficient MXScarna(seed): 0.749 RDfolder: 0.487 Sensitivity MXScarna(seed): 0.715 RDfolder: 0.421 Positive Predictive Value MXScarna(seed): 0.788 RDfolder: 0.571 Number of pairs reference - predicted secondary structure: 156 Wilcoxon single-rank test P-value: 3.56938820447e-08	211 CentroidAlifold(20) vs RDfolder Matthews Correlation Coefficient CentroidAlifold(20): 0.907 RDfolder: 0.556 Sensitivity CentroidAlifold(20): 0.844 RDfolder: 0.511 Positive Predictive Value CentroidAlifold(20): 0.977 RDfolder: 0.611 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	211 PETfold_pre2.0(20) vs RDfolder Matthews Correlation Coefficient PETfold_pre2.0(20): 0.887 RDfolder: 0.556 Sensitivity PETfold_pre2.0(20): 0.811 RDfolder: 0.511 Positive Predictive Value PETfold_pre2.0(20): 0.973 RDfolder: 0.611 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	211 MXScarna(20) vs RDfolder Matthews Correlation Coefficient MXScarna(20): 0.873 RDfolder: 0.556 Sensitivity MXScarna(20): 0.835 RDfolder: 0.511 Positive Predictive Value MXScarna(20): 0.915 RDfolder: 0.611 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	208 PPfold(20) vs RDfolder Matthews Correlation Coefficient PPfold(20): 0.884 RDfolder: 0.562 Sensitivity PPfold(20): 0.800 RDfolder: 0.517 Positive Predictive Value PPfold(20): 0.979 RDfolder: 0.618 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	211 RNAalifold(20) vs RDfolder Matthews Correlation Coefficient RNAalifold(20): 0.883 RDfolder: 0.556 Sensitivity RNAalifold(20): 0.795 RDfolder: 0.511 Positive Predictive Value RNAalifold(20): 0.982 RDfolder: 0.611 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	211 RSpredict(20) vs RDfolder Matthews Correlation Coefficient RSpredict(20): 0.821 RDfolder: 0.556 Sensitivity RSpredict(20): 0.738 RDfolder: 0.511 Positive Predictive Value RSpredict(20): 0.917 RDfolder: 0.611 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 IPknot vs RDfolder Matthews Correlation Coefficient IPknot: 0.689 RDfolder: 0.520 Sensitivity IPknot: 0.655 RDfolder: 0.464 Positive Predictive Value IPknot: 0.731 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	209 Multilign(20) vs RDfolder Matthews Correlation Coefficient Multilign(20): 0.829 RDfolder: 0.561 Sensitivity Multilign(20): 0.758 RDfolder: 0.517 Positive Predictive Value Multilign(20): 0.910 RDfolder: 0.616 Number of pairs reference - predicted secondary structure: 209 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 CentroidFold vs RDfolder Matthews Correlation Coefficient CentroidFold: 0.658 RDfolder: 0.520 Sensitivity CentroidFold: 0.621 RDfolder: 0.464 Positive Predictive Value CentroidFold: 0.703 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 Contrafold vs RDfolder Matthews Correlation Coefficient Contrafold: 0.657 RDfolder: 0.520 Sensitivity Contrafold: 0.646 RDfolder: 0.464 Positive Predictive Value Contrafold: 0.675 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	208 RNASampler(20) vs RDfolder Matthews Correlation Coefficient RNASampler(20): 0.859 RDfolder: 0.560 Sensitivity RNASampler(20): 0.761 RDfolder: 0.516 Positive Predictive Value RNASampler(20): 0.971 RDfolder: 0.614 Number of pairs reference - predicted secondary structure: 208 Wilcoxon single-rank test P-value: 3.56938820447e-08	211 Murlet(20) vs RDfolder Matthews Correlation Coefficient Murlet(20): 0.780 RDfolder: 0.556 Sensitivity Murlet(20): 0.685 RDfolder: 0.511 Positive Predictive Value Murlet(20): 0.892 RDfolder: 0.611 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	62 CMfinder(seed) vs RDfolder Matthews Correlation Coefficient CMfinder(seed): 0.512 RDfolder: 0.317 Sensitivity CMfinder(seed): 0.382 RDfolder: 0.254 Positive Predictive Value CMfinder(seed): 0.696 RDfolder: 0.411 Number of pairs reference - predicted secondary structure: 62 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 MaxExpect vs RDfolder Matthews Correlation Coefficient MaxExpect: 0.641 RDfolder: 0.520 Sensitivity MaxExpect: 0.622 RDfolder: 0.464 Positive Predictive Value MaxExpect: 0.667 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	211 CMfinder(20) vs RDfolder Matthews Correlation Coefficient CMfinder(20): 0.792 RDfolder: 0.556 Sensitivity CMfinder(20): 0.679 RDfolder: 0.511 Positive Predictive Value CMfinder(20): 0.927 RDfolder: 0.611 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	692 CRWrnafold vs RDfolder Matthews Correlation Coefficient CRWrnafold: 0.615 RDfolder: 0.520 Sensitivity CRWrnafold: 0.601 RDfolder: 0.464 Positive Predictive Value CRWrnafold: 0.635 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 692 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 ProbKnot vs RDfolder Matthews Correlation Coefficient ProbKnot: 0.640 RDfolder: 0.520 Sensitivity ProbKnot: 0.632 RDfolder: 0.464 Positive Predictive Value ProbKnot: 0.656 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	211 Mastr(20) vs RDfolder Matthews Correlation Coefficient Mastr(20): 0.730 RDfolder: 0.556 Sensitivity Mastr(20): 0.677 RDfolder: 0.511 Positive Predictive Value Mastr(20): 0.790 RDfolder: 0.611 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 Fold vs RDfolder Matthews Correlation Coefficient Fold: 0.633 RDfolder: 0.520 Sensitivity Fold: 0.623 RDfolder: 0.464 Positive Predictive Value Fold: 0.650 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 UNAFold vs RDfolder Matthews Correlation Coefficient UNAFold: 0.597 RDfolder: 0.520 Sensitivity UNAFold: 0.584 RDfolder: 0.464 Positive Predictive Value UNAFold: 0.617 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 PknotsRG vs RDfolder Matthews Correlation Coefficient PknotsRG: 0.605 RDfolder: 0.520 Sensitivity PknotsRG: 0.598 RDfolder: 0.464 Positive Predictive Value PknotsRG: 0.619 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 Sfold vs RDfolder Matthews Correlation Coefficient Sfold: 0.603 RDfolder: 0.520 Sensitivity Sfold: 0.566 RDfolder: 0.464 Positive Predictive Value Sfold: 0.649 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	134 RNAalifold(seed) vs RDfolder Matthews Correlation Coefficient RNAalifold(seed): 0.617 RDfolder: 0.448 Sensitivity RNAalifold(seed): 0.418 RDfolder: 0.382 Positive Predictive Value RNAalifold(seed): 0.917 RDfolder: 0.533 Number of pairs reference - predicted secondary structure: 134 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 RNAsubopt vs RDfolder Matthews Correlation Coefficient RNAsubopt: 0.608 RDfolder: 0.520 Sensitivity RNAsubopt: 0.603 RDfolder: 0.464 Positive Predictive Value RNAsubopt: 0.621 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 HotKnots vs RDfolder Matthews Correlation Coefficient HotKnots: 0.594 RDfolder: 0.520 Sensitivity HotKnots: 0.590 RDfolder: 0.464 Positive Predictive Value HotKnots: 0.605 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 RNAfold vs RDfolder Matthews Correlation Coefficient RNAfold: 0.596 RDfolder: 0.520 Sensitivity RNAfold: 0.589 RDfolder: 0.464 Positive Predictive Value RNAfold: 0.611 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 RNAshapes vs RDfolder Matthews Correlation Coefficient RNAshapes: 0.596 RDfolder: 0.520 Sensitivity RNAshapes: 0.587 RDfolder: 0.464 Positive Predictive Value RNAshapes: 0.612 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	69 RNASampler(seed) vs RDfolder Matthews Correlation Coefficient RNASampler(seed): 0.455 RDfolder: 0.357 Sensitivity RNASampler(seed): 0.284 RDfolder: 0.288 Positive Predictive Value RNASampler(seed): 0.738 RDfolder: 0.456 Number of pairs reference - predicted secondary structure: 69 Wilcoxon single-rank test P-value: 3.56938820447e-08	402 Afold vs RDfolder Matthews Correlation Coefficient Afold: 0.542 RDfolder: 0.482 Sensitivity Afold: 0.522 RDfolder: 0.417 Positive Predictive Value Afold: 0.574 RDfolder: 0.569 Number of pairs reference - predicted secondary structure: 402 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 Pknots vs RDfolder Matthews Correlation Coefficient Pknots: 0.610 RDfolder: 0.520 Sensitivity Pknots: 0.599 RDfolder: 0.464 Positive Predictive Value Pknots: 0.629 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 McQFold vs RDfolder Matthews Correlation Coefficient McQFold: 0.653 RDfolder: 0.520 Sensitivity McQFold: 0.624 RDfolder: 0.464 Positive Predictive Value McQFold: 0.689 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	211 Carnac(20) vs RDfolder Matthews Correlation Coefficient Carnac(20): 0.744 RDfolder: 0.556 Sensitivity Carnac(20): 0.591 RDfolder: 0.511 Positive Predictive Value Carnac(20): 0.940 RDfolder: 0.611 Number of pairs reference - predicted secondary structure: 211 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 RNASLOpt vs RDfolder Matthews Correlation Coefficient RNASLOpt: 0.612 RDfolder: 0.520 Sensitivity RNASLOpt: 0.567 RDfolder: 0.464 Positive Predictive Value RNASLOpt: 0.667 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	673 Cylofold vs RDfolder Matthews Correlation Coefficient Cylofold: 0.621 RDfolder: 0.528 Sensitivity Cylofold: 0.599 RDfolder: 0.470 Positive Predictive Value Cylofold: 0.650 RDfolder: 0.601 Number of pairs reference - predicted secondary structure: 673 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Multilign(seed) vs RDfolder Matthews Correlation Coefficient Multilign(seed): 0.485 RDfolder: 0.480 Sensitivity Multilign(seed): 0.386 RDfolder: 0.391 Positive Predictive Value Multilign(seed): 0.619 RDfolder: 0.600 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 0.0656750159858	693 RNAwolf vs RDfolder Matthews Correlation Coefficient RNAwolf: 0.551 RDfolder: 0.520 Sensitivity RNAwolf: 0.555 RDfolder: 0.464 Positive Predictive Value RNAwolf: 0.555 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	29 RDfolder vs PPfold(seed) Matthews Correlation Coefficient RDfolder: 0.528 PPfold(seed): 0.501 Sensitivity RDfolder: 0.462 PPfold(seed): 0.297 Positive Predictive Value RDfolder: 0.612 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 29 Wilcoxon single-rank test P-value: 4.8721359809e-07	71 Murlet(seed) vs RDfolder Matthews Correlation Coefficient Murlet(seed): 0.451 RDfolder: 0.361 Sensitivity Murlet(seed): 0.267 RDfolder: 0.294 Positive Predictive Value Murlet(seed): 0.771 RDfolder: 0.455 Number of pairs reference - predicted secondary structure: 71 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 Alterna vs RDfolder Matthews Correlation Coefficient Alterna: 0.552 RDfolder: 0.520 Sensitivity Alterna: 0.547 RDfolder: 0.464 Positive Predictive Value Alterna: 0.566 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	89 Carnac(seed) vs RDfolder Matthews Correlation Coefficient Carnac(seed): 0.503 RDfolder: 0.434 Sensitivity Carnac(seed): 0.281 RDfolder: 0.361 Positive Predictive Value Carnac(seed): 0.907 RDfolder: 0.532 Number of pairs reference - predicted secondary structure: 89 Wilcoxon single-rank test P-value: 3.56938820447e-08	693 Vsfold4 vs RDfolder Matthews Correlation Coefficient Vsfold4: 0.596 RDfolder: 0.520 Sensitivity Vsfold4: 0.547 RDfolder: 0.464 Positive Predictive Value Vsfold4: 0.656 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08	145 RSpredict(seed) vs RDfolder Matthews Correlation Coefficient RSpredict(seed): 0.472 RDfolder: 0.468 Sensitivity RSpredict(seed): 0.337 RDfolder: 0.402 Positive Predictive Value RSpredict(seed): 0.669 RDfolder: 0.552 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 0.0215355173778	693 Vsfold5 vs RDfolder Matthews Correlation Coefficient Vsfold5: 0.582 RDfolder: 0.520 Sensitivity Vsfold5: 0.551 RDfolder: 0.464 Positive Predictive Value Vsfold5: 0.623 RDfolder: 0.592 Number of pairs reference - predicted secondary structure: 693 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ RDfolder vs MCFold Matthews Correlation Coefficient RDfolder: 0.515 MCFold: 0.468 Sensitivity RDfolder: 0.457 MCFold: 0.524 Positive Predictive Value RDfolder: 0.589 MCFold: 0.428 Number of pairs reference - predicted secondary structure: 649 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RDfolder vs NanoFolder Matthews Correlation Coefficient RDfolder: 0.477 NanoFolder: 0.390 Sensitivity RDfolder: 0.419 NanoFolder: 0.447 Positive Predictive Value RDfolder: 0.550 NanoFolder: 0.350 Number of pairs reference - predicted secondary structure: 87 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ RDfolder vs Mastr(seed) Matthews Correlation Coefficient RDfolder: 0.485 Mastr(seed): 0.309 Sensitivity RDfolder: 0.420 Mastr(seed): 0.118 Positive Predictive Value RDfolder: 0.569 Mastr(seed): 0.815 Number of pairs reference - predicted secondary structure: 157 Wilcoxon single-rank test P-value: 3.56938820447e-08
MCFold	761 ContextFold vs MCFold Matthews Correlation Coefficient ContextFold: 0.771 MCFold: 0.473 Sensitivity ContextFold: 0.731 MCFold: 0.524 Positive Predictive Value ContextFold: 0.817 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	258 TurboFold(20) vs MCFold Matthews Correlation Coefficient TurboFold(20): 0.885 MCFold: 0.500 Sensitivity TurboFold(20): 0.859 MCFold: 0.559 Positive Predictive Value TurboFold(20): 0.914 MCFold: 0.453 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	185 CentroidAlifold(seed) vs MCFold Matthews Correlation Coefficient CentroidAlifold(seed): 0.786 MCFold: 0.472 Sensitivity CentroidAlifold(seed): 0.691 MCFold: 0.523 Positive Predictive Value CentroidAlifold(seed): 0.896 MCFold: 0.432 Number of pairs reference - predicted secondary structure: 185 Wilcoxon single-rank test P-value: 3.56938820447e-08	761 CentroidHomfold‑LAST vs MCFold Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.736 MCFold: 0.473 Sensitivity CentroidHomfold‑LAST: 0.671 MCFold: 0.524 Positive Predictive Value CentroidHomfold‑LAST: 0.812 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	407 PETfold_pre2.0(seed) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.880 MCFold: 0.480 Sensitivity PETfold_pre2.0(seed): 0.828 MCFold: 0.542 Positive Predictive Value PETfold_pre2.0(seed): 0.938 MCFold: 0.431 Number of pairs reference - predicted secondary structure: 407 Wilcoxon single-rank test P-value: 3.56938820447e-08	30 TurboFold(seed) vs MCFold Matthews Correlation Coefficient TurboFold(seed): 0.788 MCFold: 0.459 Sensitivity TurboFold(seed): 0.752 MCFold: 0.515 Positive Predictive Value TurboFold(seed): 0.828 MCFold: 0.417 Number of pairs reference - predicted secondary structure: 30 Wilcoxon single-rank test P-value: 3.56938820447e-08	198 MXScarna(seed) vs MCFold Matthews Correlation Coefficient MXScarna(seed): 0.752 MCFold: 0.472 Sensitivity MXScarna(seed): 0.715 MCFold: 0.525 Positive Predictive Value MXScarna(seed): 0.793 MCFold: 0.432 Number of pairs reference - predicted secondary structure: 198 Wilcoxon single-rank test P-value: 3.56938820447e-08	258 CentroidAlifold(20) vs MCFold Matthews Correlation Coefficient CentroidAlifold(20): 0.840 MCFold: 0.500 Sensitivity CentroidAlifold(20): 0.742 MCFold: 0.559 Positive Predictive Value CentroidAlifold(20): 0.953 MCFold: 0.453 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	258 PETfold_pre2.0(20) vs MCFold Matthews Correlation Coefficient PETfold_pre2.0(20): 0.838 MCFold: 0.500 Sensitivity PETfold_pre2.0(20): 0.724 MCFold: 0.559 Positive Predictive Value PETfold_pre2.0(20): 0.973 MCFold: 0.453 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	258 MXScarna(20) vs MCFold Matthews Correlation Coefficient MXScarna(20): 0.833 MCFold: 0.500 Sensitivity MXScarna(20): 0.786 MCFold: 0.559 Positive Predictive Value MXScarna(20): 0.886 MCFold: 0.453 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	254 PPfold(20) vs MCFold Matthews Correlation Coefficient PPfold(20): 0.830 MCFold: 0.500 Sensitivity PPfold(20): 0.707 MCFold: 0.560 Positive Predictive Value PPfold(20): 0.976 MCFold: 0.454 Number of pairs reference - predicted secondary structure: 254 Wilcoxon single-rank test P-value: 3.56938820447e-08	258 RNAalifold(20) vs MCFold Matthews Correlation Coefficient RNAalifold(20): 0.817 MCFold: 0.500 Sensitivity RNAalifold(20): 0.689 MCFold: 0.559 Positive Predictive Value RNAalifold(20): 0.970 MCFold: 0.453 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	258 RSpredict(20) vs MCFold Matthews Correlation Coefficient RSpredict(20): 0.789 MCFold: 0.500 Sensitivity RSpredict(20): 0.690 MCFold: 0.559 Positive Predictive Value RSpredict(20): 0.905 MCFold: 0.453 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	761 IPknot vs MCFold Matthews Correlation Coefficient IPknot: 0.689 MCFold: 0.473 Sensitivity IPknot: 0.654 MCFold: 0.524 Positive Predictive Value IPknot: 0.730 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	251 Multilign(20) vs MCFold Matthews Correlation Coefficient Multilign(20): 0.774 MCFold: 0.498 Sensitivity Multilign(20): 0.681 MCFold: 0.558 Positive Predictive Value Multilign(20): 0.883 MCFold: 0.451 Number of pairs reference - predicted secondary structure: 251 Wilcoxon single-rank test P-value: 3.56938820447e-08	761 CentroidFold vs MCFold Matthews Correlation Coefficient CentroidFold: 0.655 MCFold: 0.473 Sensitivity CentroidFold: 0.618 MCFold: 0.524 Positive Predictive Value CentroidFold: 0.699 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	761 Contrafold vs MCFold Matthews Correlation Coefficient Contrafold: 0.654 MCFold: 0.473 Sensitivity Contrafold: 0.642 MCFold: 0.524 Positive Predictive Value Contrafold: 0.672 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	254 RNASampler(20) vs MCFold Matthews Correlation Coefficient RNASampler(20): 0.771 MCFold: 0.500 Sensitivity RNASampler(20): 0.623 MCFold: 0.560 Positive Predictive Value RNASampler(20): 0.956 MCFold: 0.454 Number of pairs reference - predicted secondary structure: 254 Wilcoxon single-rank test P-value: 3.56938820447e-08	257 Murlet(20) vs MCFold Matthews Correlation Coefficient Murlet(20): 0.748 MCFold: 0.501 Sensitivity Murlet(20): 0.616 MCFold: 0.560 Positive Predictive Value Murlet(20): 0.911 MCFold: 0.454 Number of pairs reference - predicted secondary structure: 257 Wilcoxon single-rank test P-value: 3.56938820447e-08	68 CMfinder(seed) vs MCFold Matthews Correlation Coefficient CMfinder(seed): 0.555 MCFold: 0.396 Sensitivity CMfinder(seed): 0.421 MCFold: 0.436 Positive Predictive Value CMfinder(seed): 0.736 MCFold: 0.367 Number of pairs reference - predicted secondary structure: 68 Wilcoxon single-rank test P-value: 3.56938820447e-08	761 MaxExpect vs MCFold Matthews Correlation Coefficient MaxExpect: 0.642 MCFold: 0.473 Sensitivity MaxExpect: 0.623 MCFold: 0.524 Positive Predictive Value MaxExpect: 0.666 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	254 CMfinder(20) vs MCFold Matthews Correlation Coefficient CMfinder(20): 0.738 MCFold: 0.498 Sensitivity CMfinder(20): 0.608 MCFold: 0.558 Positive Predictive Value CMfinder(20): 0.898 MCFold: 0.452 Number of pairs reference - predicted secondary structure: 254 Wilcoxon single-rank test P-value: 3.56938820447e-08	760 CRWrnafold vs MCFold Matthews Correlation Coefficient CRWrnafold: 0.629 MCFold: 0.473 Sensitivity CRWrnafold: 0.614 MCFold: 0.524 Positive Predictive Value CRWrnafold: 0.649 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 760 Wilcoxon single-rank test P-value: 3.56938820447e-08	761 ProbKnot vs MCFold Matthews Correlation Coefficient ProbKnot: 0.639 MCFold: 0.473 Sensitivity ProbKnot: 0.628 MCFold: 0.524 Positive Predictive Value ProbKnot: 0.656 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	258 Mastr(20) vs MCFold Matthews Correlation Coefficient Mastr(20): 0.710 MCFold: 0.500 Sensitivity Mastr(20): 0.637 MCFold: 0.559 Positive Predictive Value Mastr(20): 0.796 MCFold: 0.453 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	761 Fold vs MCFold Matthews Correlation Coefficient Fold: 0.635 MCFold: 0.473 Sensitivity Fold: 0.625 MCFold: 0.524 Positive Predictive Value Fold: 0.651 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	761 UNAFold vs MCFold Matthews Correlation Coefficient UNAFold: 0.618 MCFold: 0.473 Sensitivity UNAFold: 0.601 MCFold: 0.524 Positive Predictive Value UNAFold: 0.640 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	761 PknotsRG vs MCFold Matthews Correlation Coefficient PknotsRG: 0.620 MCFold: 0.473 Sensitivity PknotsRG: 0.610 MCFold: 0.524 Positive Predictive Value PknotsRG: 0.635 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	761 Sfold vs MCFold Matthews Correlation Coefficient Sfold: 0.621 MCFold: 0.473 Sensitivity Sfold: 0.583 MCFold: 0.524 Positive Predictive Value Sfold: 0.668 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	175 RNAalifold(seed) vs MCFold Matthews Correlation Coefficient RNAalifold(seed): 0.612 MCFold: 0.476 Sensitivity RNAalifold(seed): 0.404 MCFold: 0.525 Positive Predictive Value RNAalifold(seed): 0.932 MCFold: 0.438 Number of pairs reference - predicted secondary structure: 175 Wilcoxon single-rank test P-value: 3.56938820447e-08	761 RNAsubopt vs MCFold Matthews Correlation Coefficient RNAsubopt: 0.619 MCFold: 0.473 Sensitivity RNAsubopt: 0.610 MCFold: 0.524 Positive Predictive Value RNAsubopt: 0.633 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	760 HotKnots vs MCFold Matthews Correlation Coefficient HotKnots: 0.614 MCFold: 0.473 Sensitivity HotKnots: 0.606 MCFold: 0.524 Positive Predictive Value HotKnots: 0.627 MCFold: 0.434 Number of pairs reference - predicted secondary structure: 760 Wilcoxon single-rank test P-value: 3.56938820447e-08	761 RNAfold vs MCFold Matthews Correlation Coefficient RNAfold: 0.615 MCFold: 0.473 Sensitivity RNAfold: 0.604 MCFold: 0.524 Positive Predictive Value RNAfold: 0.632 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	761 RNAshapes vs MCFold Matthews Correlation Coefficient RNAshapes: 0.617 MCFold: 0.473 Sensitivity RNAshapes: 0.605 MCFold: 0.524 Positive Predictive Value RNAshapes: 0.635 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	74 RNASampler(seed) vs MCFold Matthews Correlation Coefficient RNASampler(seed): 0.502 MCFold: 0.422 Sensitivity RNASampler(seed): 0.334 MCFold: 0.464 Positive Predictive Value RNASampler(seed): 0.760 MCFold: 0.391 Number of pairs reference - predicted secondary structure: 74 Wilcoxon single-rank test P-value: 3.56938820447e-08	472 Afold vs MCFold Matthews Correlation Coefficient Afold: 0.556 MCFold: 0.482 Sensitivity Afold: 0.538 MCFold: 0.521 Positive Predictive Value Afold: 0.581 MCFold: 0.454 Number of pairs reference - predicted secondary structure: 472 Wilcoxon single-rank test P-value: 3.56938820447e-08	653 Pknots vs MCFold Matthews Correlation Coefficient Pknots: 0.598 MCFold: 0.466 Sensitivity Pknots: 0.585 MCFold: 0.521 Positive Predictive Value Pknots: 0.620 MCFold: 0.426 Number of pairs reference - predicted secondary structure: 653 Wilcoxon single-rank test P-value: 3.56938820447e-08	761 McQFold vs MCFold Matthews Correlation Coefficient McQFold: 0.593 MCFold: 0.473 Sensitivity McQFold: 0.563 MCFold: 0.524 Positive Predictive Value McQFold: 0.631 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	258 Carnac(20) vs MCFold Matthews Correlation Coefficient Carnac(20): 0.677 MCFold: 0.500 Sensitivity Carnac(20): 0.505 MCFold: 0.559 Positive Predictive Value Carnac(20): 0.912 MCFold: 0.453 Number of pairs reference - predicted secondary structure: 258 Wilcoxon single-rank test P-value: 3.56938820447e-08	761 RNASLOpt vs MCFold Matthews Correlation Coefficient RNASLOpt: 0.577 MCFold: 0.473 Sensitivity RNASLOpt: 0.531 MCFold: 0.524 Positive Predictive Value RNASLOpt: 0.633 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	714 Cylofold vs MCFold Matthews Correlation Coefficient Cylofold: 0.584 MCFold: 0.487 Sensitivity Cylofold: 0.559 MCFold: 0.542 Positive Predictive Value Cylofold: 0.617 MCFold: 0.447 Number of pairs reference - predicted secondary structure: 714 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Multilign(seed) vs MCFold Matthews Correlation Coefficient Multilign(seed): 0.485 MCFold: 0.359 Sensitivity Multilign(seed): 0.386 MCFold: 0.419 Positive Predictive Value Multilign(seed): 0.619 MCFold: 0.319 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 2.06323189071e-08	761 RNAwolf vs MCFold Matthews Correlation Coefficient RNAwolf: 0.530 MCFold: 0.473 Sensitivity RNAwolf: 0.532 MCFold: 0.524 Positive Predictive Value RNAwolf: 0.534 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	35 MCFold vs PPfold(seed) Matthews Correlation Coefficient MCFold: 0.421 PPfold(seed): 0.417 Sensitivity MCFold: 0.478 PPfold(seed): 0.206 Positive Predictive Value MCFold: 0.378 PPfold(seed): 0.852 Number of pairs reference - predicted secondary structure: 35 Wilcoxon single-rank test P-value: 0.313407754584	78 Murlet(seed) vs MCFold Matthews Correlation Coefficient Murlet(seed): 0.431 MCFold: 0.427 Sensitivity Murlet(seed): 0.236 MCFold: 0.470 Positive Predictive Value Murlet(seed): 0.793 MCFold: 0.396 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 0.221270004692	649 Alterna vs MCFold Matthews Correlation Coefficient Alterna: 0.552 MCFold: 0.468 Sensitivity Alterna: 0.543 MCFold: 0.524 Positive Predictive Value Alterna: 0.569 MCFold: 0.428 Number of pairs reference - predicted secondary structure: 649 Wilcoxon single-rank test P-value: 3.56938820447e-08	105 MCFold vs Carnac(seed) Matthews Correlation Coefficient MCFold: 0.446 Carnac(seed): 0.444 Sensitivity MCFold: 0.494 Carnac(seed): 0.222 Positive Predictive Value MCFold: 0.411 Carnac(seed): 0.896 Number of pairs reference - predicted secondary structure: 105 Wilcoxon single-rank test P-value: 0.00911763231782	761 Vsfold4 vs MCFold Matthews Correlation Coefficient Vsfold4: 0.500 MCFold: 0.473 Sensitivity Vsfold4: 0.456 MCFold: 0.524 Positive Predictive Value Vsfold4: 0.555 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	185 MCFold vs RSpredict(seed) Matthews Correlation Coefficient MCFold: 0.472 RSpredict(seed): 0.391 Sensitivity MCFold: 0.523 RSpredict(seed): 0.265 Positive Predictive Value MCFold: 0.432 RSpredict(seed): 0.583 Number of pairs reference - predicted secondary structure: 185 Wilcoxon single-rank test P-value: 3.56938820447e-08	761 Vsfold5 vs MCFold Matthews Correlation Coefficient Vsfold5: 0.489 MCFold: 0.473 Sensitivity Vsfold5: 0.460 MCFold: 0.524 Positive Predictive Value Vsfold5: 0.527 MCFold: 0.435 Number of pairs reference - predicted secondary structure: 761 Wilcoxon single-rank test P-value: 3.56938820447e-08	649 RDfolder vs MCFold Matthews Correlation Coefficient RDfolder: 0.515 MCFold: 0.468 Sensitivity RDfolder: 0.457 MCFold: 0.524 Positive Predictive Value RDfolder: 0.589 MCFold: 0.428 Number of pairs reference - predicted secondary structure: 649 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ MCFold vs NanoFolder Matthews Correlation Coefficient MCFold: 0.456 NanoFolder: 0.352 Sensitivity MCFold: 0.509 NanoFolder: 0.404 Positive Predictive Value MCFold: 0.416 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 104 Wilcoxon single-rank test P-value: 3.56938820447e-08	+ MCFold vs Mastr(seed) Matthews Correlation Coefficient MCFold: 0.473 Mastr(seed): 0.261 Sensitivity MCFold: 0.525 Mastr(seed): 0.084 Positive Predictive Value MCFold: 0.433 Mastr(seed): 0.822 Number of pairs reference - predicted secondary structure: 199 Wilcoxon single-rank test P-value: 3.56938820447e-08
NanoFolder	117 ContextFold vs NanoFolder Matthews Correlation Coefficient ContextFold: 0.839 NanoFolder: 0.335 Sensitivity ContextFold: 0.799 NanoFolder: 0.384 Positive Predictive Value ContextFold: 0.882 NanoFolder: 0.301 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	59 TurboFold(20) vs NanoFolder Matthews Correlation Coefficient TurboFold(20): 0.888 NanoFolder: 0.337 Sensitivity TurboFold(20): 0.859 NanoFolder: 0.391 Positive Predictive Value TurboFold(20): 0.919 NanoFolder: 0.298 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 3.56938820447e-08	43 CentroidAlifold(seed) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(seed): 0.811 NanoFolder: 0.391 Sensitivity CentroidAlifold(seed): 0.730 NanoFolder: 0.446 Positive Predictive Value CentroidAlifold(seed): 0.902 NanoFolder: 0.350 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	117 CentroidHomfold‑LAST vs NanoFolder Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.760 NanoFolder: 0.335 Sensitivity CentroidHomfold‑LAST: 0.686 NanoFolder: 0.384 Positive Predictive Value CentroidHomfold‑LAST: 0.844 NanoFolder: 0.301 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	79 PETfold_pre2.0(seed) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.849 NanoFolder: 0.355 Sensitivity PETfold_pre2.0(seed): 0.777 NanoFolder: 0.415 Positive Predictive Value PETfold_pre2.0(seed): 0.929 NanoFolder: 0.312 Number of pairs reference - predicted secondary structure: 79 Wilcoxon single-rank test P-value: 3.56938820447e-08	11 TurboFold(seed) vs NanoFolder Matthews Correlation Coefficient TurboFold(seed): 0.834 NanoFolder: 0.423 Sensitivity TurboFold(seed): 0.785 NanoFolder: 0.480 Positive Predictive Value TurboFold(seed): 0.889 NanoFolder: 0.381 Number of pairs reference - predicted secondary structure: 11 Wilcoxon single-rank test P-value: 1.43692248862e-08	48 MXScarna(seed) vs NanoFolder Matthews Correlation Coefficient MXScarna(seed): 0.774 NanoFolder: 0.372 Sensitivity MXScarna(seed): 0.736 NanoFolder: 0.427 Positive Predictive Value MXScarna(seed): 0.817 NanoFolder: 0.332 Number of pairs reference - predicted secondary structure: 48 Wilcoxon single-rank test P-value: 3.56938820447e-08	59 CentroidAlifold(20) vs NanoFolder Matthews Correlation Coefficient CentroidAlifold(20): 0.794 NanoFolder: 0.337 Sensitivity CentroidAlifold(20): 0.666 NanoFolder: 0.391 Positive Predictive Value CentroidAlifold(20): 0.949 NanoFolder: 0.298 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 3.56938820447e-08	59 PETfold_pre2.0(20) vs NanoFolder Matthews Correlation Coefficient PETfold_pre2.0(20): 0.794 NanoFolder: 0.337 Sensitivity PETfold_pre2.0(20): 0.654 NanoFolder: 0.391 Positive Predictive Value PETfold_pre2.0(20): 0.967 NanoFolder: 0.298 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 3.56938820447e-08	59 MXScarna(20) vs NanoFolder Matthews Correlation Coefficient MXScarna(20): 0.812 NanoFolder: 0.337 Sensitivity MXScarna(20): 0.757 NanoFolder: 0.391 Positive Predictive Value MXScarna(20): 0.875 NanoFolder: 0.298 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 3.56938820447e-08	58 PPfold(20) vs NanoFolder Matthews Correlation Coefficient PPfold(20): 0.788 NanoFolder: 0.337 Sensitivity PPfold(20): 0.639 NanoFolder: 0.392 Positive Predictive Value PPfold(20): 0.974 NanoFolder: 0.298 Number of pairs reference - predicted secondary structure: 58 Wilcoxon single-rank test P-value: 3.56938820447e-08	59 RNAalifold(20) vs NanoFolder Matthews Correlation Coefficient RNAalifold(20): 0.767 NanoFolder: 0.337 Sensitivity RNAalifold(20): 0.614 NanoFolder: 0.391 Positive Predictive Value RNAalifold(20): 0.959 NanoFolder: 0.298 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 3.56938820447e-08	59 RSpredict(20) vs NanoFolder Matthews Correlation Coefficient RSpredict(20): 0.748 NanoFolder: 0.337 Sensitivity RSpredict(20): 0.635 NanoFolder: 0.391 Positive Predictive Value RSpredict(20): 0.886 NanoFolder: 0.298 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 3.56938820447e-08	117 IPknot vs NanoFolder Matthews Correlation Coefficient IPknot: 0.724 NanoFolder: 0.335 Sensitivity IPknot: 0.694 NanoFolder: 0.384 Positive Predictive Value IPknot: 0.759 NanoFolder: 0.301 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	57 Multilign(20) vs NanoFolder Matthews Correlation Coefficient Multilign(20): 0.743 NanoFolder: 0.337 Sensitivity Multilign(20): 0.604 NanoFolder: 0.391 Positive Predictive Value Multilign(20): 0.918 NanoFolder: 0.298 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	117 CentroidFold vs NanoFolder Matthews Correlation Coefficient CentroidFold: 0.665 NanoFolder: 0.335 Sensitivity CentroidFold: 0.635 NanoFolder: 0.384 Positive Predictive Value CentroidFold: 0.701 NanoFolder: 0.301 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	117 Contrafold vs NanoFolder Matthews Correlation Coefficient Contrafold: 0.668 NanoFolder: 0.335 Sensitivity Contrafold: 0.658 NanoFolder: 0.384 Positive Predictive Value Contrafold: 0.683 NanoFolder: 0.301 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	57 RNASampler(20) vs NanoFolder Matthews Correlation Coefficient RNASampler(20): 0.732 NanoFolder: 0.338 Sensitivity RNASampler(20): 0.555 NanoFolder: 0.392 Positive Predictive Value RNASampler(20): 0.968 NanoFolder: 0.300 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	59 Murlet(20) vs NanoFolder Matthews Correlation Coefficient Murlet(20): 0.712 NanoFolder: 0.337 Sensitivity Murlet(20): 0.555 NanoFolder: 0.391 Positive Predictive Value Murlet(20): 0.917 NanoFolder: 0.298 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 3.56938820447e-08	15 CMfinder(seed) vs NanoFolder Matthews Correlation Coefficient CMfinder(seed): 0.575 NanoFolder: 0.392 Sensitivity CMfinder(seed): 0.432 NanoFolder: 0.436 Positive Predictive Value CMfinder(seed): 0.771 NanoFolder: 0.362 Number of pairs reference - predicted secondary structure: 15 Wilcoxon single-rank test P-value: 1.82627677697e-08	117 MaxExpect vs NanoFolder Matthews Correlation Coefficient MaxExpect: 0.668 NanoFolder: 0.335 Sensitivity MaxExpect: 0.650 NanoFolder: 0.384 Positive Predictive Value MaxExpect: 0.691 NanoFolder: 0.301 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	57 CMfinder(20) vs NanoFolder Matthews Correlation Coefficient CMfinder(20): 0.689 NanoFolder: 0.333 Sensitivity CMfinder(20): 0.554 NanoFolder: 0.387 Positive Predictive Value CMfinder(20): 0.862 NanoFolder: 0.295 Number of pairs reference - predicted secondary structure: 57 Wilcoxon single-rank test P-value: 3.56938820447e-08	117 CRWrnafold vs NanoFolder Matthews Correlation Coefficient CRWrnafold: 0.671 NanoFolder: 0.335 Sensitivity CRWrnafold: 0.654 NanoFolder: 0.384 Positive Predictive Value CRWrnafold: 0.692 NanoFolder: 0.301 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	117 ProbKnot vs NanoFolder Matthews Correlation Coefficient ProbKnot: 0.671 NanoFolder: 0.335 Sensitivity ProbKnot: 0.658 NanoFolder: 0.384 Positive Predictive Value ProbKnot: 0.688 NanoFolder: 0.301 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	59 Mastr(20) vs NanoFolder Matthews Correlation Coefficient Mastr(20): 0.704 NanoFolder: 0.337 Sensitivity Mastr(20): 0.599 NanoFolder: 0.391 Positive Predictive Value Mastr(20): 0.832 NanoFolder: 0.298 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 3.56938820447e-08	117 Fold vs NanoFolder Matthews Correlation Coefficient Fold: 0.667 NanoFolder: 0.335 Sensitivity Fold: 0.655 NanoFolder: 0.384 Positive Predictive Value Fold: 0.683 NanoFolder: 0.301 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	117 UNAFold vs NanoFolder Matthews Correlation Coefficient UNAFold: 0.670 NanoFolder: 0.335 Sensitivity UNAFold: 0.654 NanoFolder: 0.384 Positive Predictive Value UNAFold: 0.691 NanoFolder: 0.301 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	117 PknotsRG vs NanoFolder Matthews Correlation Coefficient PknotsRG: 0.662 NanoFolder: 0.335 Sensitivity PknotsRG: 0.650 NanoFolder: 0.384 Positive Predictive Value PknotsRG: 0.679 NanoFolder: 0.301 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	117 Sfold vs NanoFolder Matthews Correlation Coefficient Sfold: 0.631 NanoFolder: 0.335 Sensitivity Sfold: 0.600 NanoFolder: 0.384 Positive Predictive Value Sfold: 0.668 NanoFolder: 0.301 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	43 RNAalifold(seed) vs NanoFolder Matthews Correlation Coefficient RNAalifold(seed): 0.600 NanoFolder: 0.391 Sensitivity RNAalifold(seed): 0.377 NanoFolder: 0.446 Positive Predictive Value RNAalifold(seed): 0.960 NanoFolder: 0.350 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	117 RNAsubopt vs NanoFolder Matthews Correlation Coefficient RNAsubopt: 0.640 NanoFolder: 0.335 Sensitivity RNAsubopt: 0.632 NanoFolder: 0.384 Positive Predictive Value RNAsubopt: 0.652 NanoFolder: 0.301 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	116 HotKnots vs NanoFolder Matthews Correlation Coefficient HotKnots: 0.657 NanoFolder: 0.342 Sensitivity HotKnots: 0.650 NanoFolder: 0.393 Positive Predictive Value HotKnots: 0.668 NanoFolder: 0.307 Number of pairs reference - predicted secondary structure: 116 Wilcoxon single-rank test P-value: 3.56938820447e-08	117 RNAfold vs NanoFolder Matthews Correlation Coefficient RNAfold: 0.643 NanoFolder: 0.335 Sensitivity RNAfold: 0.633 NanoFolder: 0.384 Positive Predictive Value RNAfold: 0.658 NanoFolder: 0.301 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	117 RNAshapes vs NanoFolder Matthews Correlation Coefficient RNAshapes: 0.648 NanoFolder: 0.335 Sensitivity RNAshapes: 0.635 NanoFolder: 0.384 Positive Predictive Value RNAshapes: 0.665 NanoFolder: 0.301 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	17 RNASampler(seed) vs NanoFolder Matthews Correlation Coefficient RNASampler(seed): 0.461 NanoFolder: 0.413 Sensitivity RNASampler(seed): 0.281 NanoFolder: 0.464 Positive Predictive Value RNASampler(seed): 0.763 NanoFolder: 0.375 Number of pairs reference - predicted secondary structure: 17 Wilcoxon single-rank test P-value: 4.30260184036e-08	72 Afold vs NanoFolder Matthews Correlation Coefficient Afold: 0.550 NanoFolder: 0.320 Sensitivity Afold: 0.536 NanoFolder: 0.361 Positive Predictive Value Afold: 0.570 NanoFolder: 0.293 Number of pairs reference - predicted secondary structure: 72 Wilcoxon single-rank test P-value: 3.56938820447e-08	87 Pknots vs NanoFolder Matthews Correlation Coefficient Pknots: 0.604 NanoFolder: 0.390 Sensitivity Pknots: 0.590 NanoFolder: 0.447 Positive Predictive Value Pknots: 0.625 NanoFolder: 0.350 Number of pairs reference - predicted secondary structure: 87 Wilcoxon single-rank test P-value: 3.56938820447e-08	117 McQFold vs NanoFolder Matthews Correlation Coefficient McQFold: 0.589 NanoFolder: 0.335 Sensitivity McQFold: 0.559 NanoFolder: 0.384 Positive Predictive Value McQFold: 0.626 NanoFolder: 0.301 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	59 Carnac(20) vs NanoFolder Matthews Correlation Coefficient Carnac(20): 0.668 NanoFolder: 0.337 Sensitivity Carnac(20): 0.492 NanoFolder: 0.391 Positive Predictive Value Carnac(20): 0.910 NanoFolder: 0.298 Number of pairs reference - predicted secondary structure: 59 Wilcoxon single-rank test P-value: 3.56938820447e-08	117 RNASLOpt vs NanoFolder Matthews Correlation Coefficient RNASLOpt: 0.569 NanoFolder: 0.335 Sensitivity RNASLOpt: 0.520 NanoFolder: 0.384 Positive Predictive Value RNASLOpt: 0.628 NanoFolder: 0.301 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	109 Cylofold vs NanoFolder Matthews Correlation Coefficient Cylofold: 0.567 NanoFolder: 0.349 Sensitivity Cylofold: 0.536 NanoFolder: 0.400 Positive Predictive Value Cylofold: 0.606 NanoFolder: 0.313 Number of pairs reference - predicted secondary structure: 109 Wilcoxon single-rank test P-value: 3.56938820447e-08	5 NanoFolder vs Multilign(seed) Matthews Correlation Coefficient NanoFolder: 0.560 Multilign(seed): 0.551 Sensitivity NanoFolder: 0.605 Multilign(seed): 0.457 Positive Predictive Value NanoFolder: 0.527 Multilign(seed): 0.673 Number of pairs reference - predicted secondary structure: 5 Wilcoxon single-rank test P-value: 0.0	117 RNAwolf vs NanoFolder Matthews Correlation Coefficient RNAwolf: 0.583 NanoFolder: 0.335 Sensitivity RNAwolf: 0.580 NanoFolder: 0.384 Positive Predictive Value RNAwolf: 0.593 NanoFolder: 0.301 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	9 PPfold(seed) vs NanoFolder Matthews Correlation Coefficient PPfold(seed): 0.497 NanoFolder: 0.474 Sensitivity PPfold(seed): 0.276 NanoFolder: 0.518 Positive Predictive Value PPfold(seed): 0.902 NanoFolder: 0.442 Number of pairs reference - predicted secondary structure: 9 Wilcoxon single-rank test P-value: 0.0	19 Murlet(seed) vs NanoFolder Matthews Correlation Coefficient Murlet(seed): 0.441 NanoFolder: 0.421 Sensitivity Murlet(seed): 0.213 NanoFolder: 0.471 Positive Predictive Value Murlet(seed): 0.921 NanoFolder: 0.385 Number of pairs reference - predicted secondary structure: 19 Wilcoxon single-rank test P-value: 0.000616773583101	87 Alterna vs NanoFolder Matthews Correlation Coefficient Alterna: 0.573 NanoFolder: 0.390 Sensitivity Alterna: 0.561 NanoFolder: 0.447 Positive Predictive Value Alterna: 0.593 NanoFolder: 0.350 Number of pairs reference - predicted secondary structure: 87 Wilcoxon single-rank test P-value: 3.56938820447e-08	26 Carnac(seed) vs NanoFolder Matthews Correlation Coefficient Carnac(seed): 0.502 NanoFolder: 0.469 Sensitivity Carnac(seed): 0.263 NanoFolder: 0.526 Positive Predictive Value Carnac(seed): 0.964 NanoFolder: 0.425 Number of pairs reference - predicted secondary structure: 26 Wilcoxon single-rank test P-value: 5.19332990918e-08	117 Vsfold4 vs NanoFolder Matthews Correlation Coefficient Vsfold4: 0.436 NanoFolder: 0.335 Sensitivity Vsfold4: 0.399 NanoFolder: 0.384 Positive Predictive Value Vsfold4: 0.485 NanoFolder: 0.301 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	43 NanoFolder vs RSpredict(seed) Matthews Correlation Coefficient NanoFolder: 0.391 RSpredict(seed): 0.338 Sensitivity NanoFolder: 0.446 RSpredict(seed): 0.215 Positive Predictive Value NanoFolder: 0.350 RSpredict(seed): 0.539 Number of pairs reference - predicted secondary structure: 43 Wilcoxon single-rank test P-value: 3.56938820447e-08	117 Vsfold5 vs NanoFolder Matthews Correlation Coefficient Vsfold5: 0.417 NanoFolder: 0.335 Sensitivity Vsfold5: 0.389 NanoFolder: 0.384 Positive Predictive Value Vsfold5: 0.455 NanoFolder: 0.301 Number of pairs reference - predicted secondary structure: 117 Wilcoxon single-rank test P-value: 3.56938820447e-08	87 RDfolder vs NanoFolder Matthews Correlation Coefficient RDfolder: 0.477 NanoFolder: 0.390 Sensitivity RDfolder: 0.419 NanoFolder: 0.447 Positive Predictive Value RDfolder: 0.550 NanoFolder: 0.350 Number of pairs reference - predicted secondary structure: 87 Wilcoxon single-rank test P-value: 3.56938820447e-08	104 MCFold vs NanoFolder Matthews Correlation Coefficient MCFold: 0.456 NanoFolder: 0.352 Sensitivity MCFold: 0.509 NanoFolder: 0.404 Positive Predictive Value MCFold: 0.416 NanoFolder: 0.316 Number of pairs reference - predicted secondary structure: 104 Wilcoxon single-rank test P-value: 3.56938820447e-08		+ NanoFolder vs Mastr(seed) Matthews Correlation Coefficient NanoFolder: 0.369 Mastr(seed): 0.191 Sensitivity NanoFolder: 0.424 Mastr(seed): 0.055 Positive Predictive Value NanoFolder: 0.330 Mastr(seed): 0.673 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08
Mastr(seed)	234 ContextFold vs Mastr(seed) Matthews Correlation Coefficient ContextFold: 0.844 Mastr(seed): 0.263 Sensitivity ContextFold: 0.817 Mastr(seed): 0.089 Positive Predictive Value ContextFold: 0.874 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08	154 TurboFold(20) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(20): 0.839 Mastr(seed): 0.265 Sensitivity TurboFold(20): 0.818 Mastr(seed): 0.087 Positive Predictive Value TurboFold(20): 0.863 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 154 Wilcoxon single-rank test P-value: 3.56938820447e-08	216 CentroidAlifold(seed) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(seed): 0.790 Mastr(seed): 0.276 Sensitivity CentroidAlifold(seed): 0.699 Mastr(seed): 0.097 Positive Predictive Value CentroidAlifold(seed): 0.896 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	234 CentroidHomfold‑LAST vs Mastr(seed) Matthews Correlation Coefficient CentroidHomfold‑LAST: 0.801 Mastr(seed): 0.263 Sensitivity CentroidHomfold‑LAST: 0.744 Mastr(seed): 0.089 Positive Predictive Value CentroidHomfold‑LAST: 0.865 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08	231 PETfold_pre2.0(seed) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(seed): 0.769 Mastr(seed): 0.266 Sensitivity PETfold_pre2.0(seed): 0.679 Mastr(seed): 0.090 Positive Predictive Value PETfold_pre2.0(seed): 0.874 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 231 Wilcoxon single-rank test P-value: 3.56938820447e-08	33 TurboFold(seed) vs Mastr(seed) Matthews Correlation Coefficient TurboFold(seed): 0.798 Mastr(seed): 0.330 Sensitivity TurboFold(seed): 0.766 Mastr(seed): 0.154 Positive Predictive Value TurboFold(seed): 0.835 Mastr(seed): 0.714 Number of pairs reference - predicted secondary structure: 33 Wilcoxon single-rank test P-value: 3.56938820447e-08	233 MXScarna(seed) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(seed): 0.750 Mastr(seed): 0.264 Sensitivity MXScarna(seed): 0.712 Mastr(seed): 0.089 Positive Predictive Value MXScarna(seed): 0.793 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 233 Wilcoxon single-rank test P-value: 3.56938820447e-08	154 CentroidAlifold(20) vs Mastr(seed) Matthews Correlation Coefficient CentroidAlifold(20): 0.727 Mastr(seed): 0.265 Sensitivity CentroidAlifold(20): 0.560 Mastr(seed): 0.087 Positive Predictive Value CentroidAlifold(20): 0.946 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 154 Wilcoxon single-rank test P-value: 3.56938820447e-08	154 PETfold_pre2.0(20) vs Mastr(seed) Matthews Correlation Coefficient PETfold_pre2.0(20): 0.676 Mastr(seed): 0.265 Sensitivity PETfold_pre2.0(20): 0.486 Mastr(seed): 0.087 Positive Predictive Value PETfold_pre2.0(20): 0.943 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 154 Wilcoxon single-rank test P-value: 3.56938820447e-08	154 MXScarna(20) vs Mastr(seed) Matthews Correlation Coefficient MXScarna(20): 0.779 Mastr(seed): 0.265 Sensitivity MXScarna(20): 0.705 Mastr(seed): 0.087 Positive Predictive Value MXScarna(20): 0.864 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 154 Wilcoxon single-rank test P-value: 3.56938820447e-08	148 PPfold(20) vs Mastr(seed) Matthews Correlation Coefficient PPfold(20): 0.662 Mastr(seed): 0.271 Sensitivity PPfold(20): 0.463 Mastr(seed): 0.091 Positive Predictive Value PPfold(20): 0.948 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 148 Wilcoxon single-rank test P-value: 3.56938820447e-08	154 RNAalifold(20) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(20): 0.671 Mastr(seed): 0.265 Sensitivity RNAalifold(20): 0.478 Mastr(seed): 0.087 Positive Predictive Value RNAalifold(20): 0.944 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 154 Wilcoxon single-rank test P-value: 3.56938820447e-08	154 RSpredict(20) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(20): 0.723 Mastr(seed): 0.265 Sensitivity RSpredict(20): 0.602 Mastr(seed): 0.087 Positive Predictive Value RSpredict(20): 0.871 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 154 Wilcoxon single-rank test P-value: 3.56938820447e-08	234 IPknot vs Mastr(seed) Matthews Correlation Coefficient IPknot: 0.736 Mastr(seed): 0.263 Sensitivity IPknot: 0.711 Mastr(seed): 0.089 Positive Predictive Value IPknot: 0.764 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08	145 Multilign(20) vs Mastr(seed) Matthews Correlation Coefficient Multilign(20): 0.625 Mastr(seed): 0.276 Sensitivity Multilign(20): 0.483 Mastr(seed): 0.094 Positive Predictive Value Multilign(20): 0.814 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 145 Wilcoxon single-rank test P-value: 3.56938820447e-08	234 CentroidFold vs Mastr(seed) Matthews Correlation Coefficient CentroidFold: 0.699 Mastr(seed): 0.263 Sensitivity CentroidFold: 0.665 Mastr(seed): 0.089 Positive Predictive Value CentroidFold: 0.738 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08	234 Contrafold vs Mastr(seed) Matthews Correlation Coefficient Contrafold: 0.693 Mastr(seed): 0.263 Sensitivity Contrafold: 0.682 Mastr(seed): 0.089 Positive Predictive Value Contrafold: 0.707 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08	150 RNASampler(20) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(20): 0.634 Mastr(seed): 0.269 Sensitivity RNASampler(20): 0.430 Mastr(seed): 0.089 Positive Predictive Value RNASampler(20): 0.940 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 150 Wilcoxon single-rank test P-value: 3.56938820447e-08	153 Murlet(20) vs Mastr(seed) Matthews Correlation Coefficient Murlet(20): 0.626 Mastr(seed): 0.266 Sensitivity Murlet(20): 0.430 Mastr(seed): 0.087 Positive Predictive Value Murlet(20): 0.916 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 153 Wilcoxon single-rank test P-value: 3.56938820447e-08	78 CMfinder(seed) vs Mastr(seed) Matthews Correlation Coefficient CMfinder(seed): 0.571 Mastr(seed): 0.504 Sensitivity CMfinder(seed): 0.439 Mastr(seed): 0.320 Positive Predictive Value CMfinder(seed): 0.747 Mastr(seed): 0.798 Number of pairs reference - predicted secondary structure: 78 Wilcoxon single-rank test P-value: 3.56938820447e-08	234 MaxExpect vs Mastr(seed) Matthews Correlation Coefficient MaxExpect: 0.691 Mastr(seed): 0.263 Sensitivity MaxExpect: 0.680 Mastr(seed): 0.089 Positive Predictive Value MaxExpect: 0.705 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08	150 CMfinder(20) vs Mastr(seed) Matthews Correlation Coefficient CMfinder(20): 0.665 Mastr(seed): 0.270 Sensitivity CMfinder(20): 0.518 Mastr(seed): 0.090 Positive Predictive Value CMfinder(20): 0.858 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 150 Wilcoxon single-rank test P-value: 3.56938820447e-08	234 CRWrnafold vs Mastr(seed) Matthews Correlation Coefficient CRWrnafold: 0.702 Mastr(seed): 0.263 Sensitivity CRWrnafold: 0.694 Mastr(seed): 0.089 Positive Predictive Value CRWrnafold: 0.714 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08	234 ProbKnot vs Mastr(seed) Matthews Correlation Coefficient ProbKnot: 0.684 Mastr(seed): 0.263 Sensitivity ProbKnot: 0.678 Mastr(seed): 0.089 Positive Predictive Value ProbKnot: 0.694 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08	154 Mastr(20) vs Mastr(seed) Matthews Correlation Coefficient Mastr(20): 0.680 Mastr(seed): 0.265 Sensitivity Mastr(20): 0.549 Mastr(seed): 0.087 Positive Predictive Value Mastr(20): 0.845 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 154 Wilcoxon single-rank test P-value: 3.56938820447e-08	234 Fold vs Mastr(seed) Matthews Correlation Coefficient Fold: 0.691 Mastr(seed): 0.263 Sensitivity Fold: 0.690 Mastr(seed): 0.089 Positive Predictive Value Fold: 0.697 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08	234 UNAFold vs Mastr(seed) Matthews Correlation Coefficient UNAFold: 0.690 Mastr(seed): 0.263 Sensitivity UNAFold: 0.684 Mastr(seed): 0.089 Positive Predictive Value UNAFold: 0.700 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08	234 PknotsRG vs Mastr(seed) Matthews Correlation Coefficient PknotsRG: 0.693 Mastr(seed): 0.263 Sensitivity PknotsRG: 0.692 Mastr(seed): 0.089 Positive Predictive Value PknotsRG: 0.697 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08	234 Sfold vs Mastr(seed) Matthews Correlation Coefficient Sfold: 0.680 Mastr(seed): 0.263 Sensitivity Sfold: 0.648 Mastr(seed): 0.089 Positive Predictive Value Sfold: 0.718 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08	205 RNAalifold(seed) vs Mastr(seed) Matthews Correlation Coefficient RNAalifold(seed): 0.610 Mastr(seed): 0.282 Sensitivity RNAalifold(seed): 0.404 Mastr(seed): 0.102 Positive Predictive Value RNAalifold(seed): 0.923 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 205 Wilcoxon single-rank test P-value: 3.56938820447e-08	234 RNAsubopt vs Mastr(seed) Matthews Correlation Coefficient RNAsubopt: 0.652 Mastr(seed): 0.263 Sensitivity RNAsubopt: 0.651 Mastr(seed): 0.089 Positive Predictive Value RNAsubopt: 0.656 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08	230 HotKnots vs Mastr(seed) Matthews Correlation Coefficient HotKnots: 0.677 Mastr(seed): 0.267 Sensitivity HotKnots: 0.678 Mastr(seed): 0.091 Positive Predictive Value HotKnots: 0.680 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 230 Wilcoxon single-rank test P-value: 3.56938820447e-08	234 RNAfold vs Mastr(seed) Matthews Correlation Coefficient RNAfold: 0.681 Mastr(seed): 0.263 Sensitivity RNAfold: 0.678 Mastr(seed): 0.089 Positive Predictive Value RNAfold: 0.688 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08	234 RNAshapes vs Mastr(seed) Matthews Correlation Coefficient RNAshapes: 0.669 Mastr(seed): 0.263 Sensitivity RNAshapes: 0.666 Mastr(seed): 0.089 Positive Predictive Value RNAshapes: 0.676 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08	86 RNASampler(seed) vs Mastr(seed) Matthews Correlation Coefficient RNASampler(seed): 0.557 Mastr(seed): 0.490 Sensitivity RNASampler(seed): 0.389 Mastr(seed): 0.307 Positive Predictive Value RNASampler(seed): 0.802 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 86 Wilcoxon single-rank test P-value: 3.56938820447e-08	167 Afold vs Mastr(seed) Matthews Correlation Coefficient Afold: 0.641 Mastr(seed): 0.305 Sensitivity Afold: 0.637 Mastr(seed): 0.119 Positive Predictive Value Afold: 0.649 Mastr(seed): 0.787 Number of pairs reference - predicted secondary structure: 167 Wilcoxon single-rank test P-value: 3.56938820447e-08	158 Pknots vs Mastr(seed) Matthews Correlation Coefficient Pknots: 0.533 Mastr(seed): 0.307 Sensitivity Pknots: 0.528 Mastr(seed): 0.117 Positive Predictive Value Pknots: 0.545 Mastr(seed): 0.815 Number of pairs reference - predicted secondary structure: 158 Wilcoxon single-rank test P-value: 3.56938820447e-08	234 McQFold vs Mastr(seed) Matthews Correlation Coefficient McQFold: 0.565 Mastr(seed): 0.263 Sensitivity McQFold: 0.541 Mastr(seed): 0.089 Positive Predictive Value McQFold: 0.595 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08	154 Carnac(20) vs Mastr(seed) Matthews Correlation Coefficient Carnac(20): 0.512 Mastr(seed): 0.265 Sensitivity Carnac(20): 0.304 Mastr(seed): 0.087 Positive Predictive Value Carnac(20): 0.866 Mastr(seed): 0.817 Number of pairs reference - predicted secondary structure: 154 Wilcoxon single-rank test P-value: 3.56938820447e-08	234 RNASLOpt vs Mastr(seed) Matthews Correlation Coefficient RNASLOpt: 0.573 Mastr(seed): 0.263 Sensitivity RNASLOpt: 0.526 Mastr(seed): 0.089 Positive Predictive Value RNASLOpt: 0.629 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08	215 Cylofold vs Mastr(seed) Matthews Correlation Coefficient Cylofold: 0.520 Mastr(seed): 0.285 Sensitivity Cylofold: 0.495 Mastr(seed): 0.101 Positive Predictive Value Cylofold: 0.553 Mastr(seed): 0.807 Number of pairs reference - predicted secondary structure: 215 Wilcoxon single-rank test P-value: 3.56938820447e-08	13 Mastr(seed) vs Multilign(seed) Matthews Correlation Coefficient Mastr(seed): 0.503 Multilign(seed): 0.485 Sensitivity Mastr(seed): 0.372 Multilign(seed): 0.386 Positive Predictive Value Mastr(seed): 0.690 Multilign(seed): 0.619 Number of pairs reference - predicted secondary structure: 13 Wilcoxon single-rank test P-value: 4.84476306662e-07	234 RNAwolf vs Mastr(seed) Matthews Correlation Coefficient RNAwolf: 0.522 Mastr(seed): 0.263 Sensitivity RNAwolf: 0.528 Mastr(seed): 0.089 Positive Predictive Value RNAwolf: 0.522 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08	40 PPfold(seed) vs Mastr(seed) Matthews Correlation Coefficient PPfold(seed): 0.380 Mastr(seed): 0.299 Sensitivity PPfold(seed): 0.170 Mastr(seed): 0.120 Positive Predictive Value PPfold(seed): 0.852 Mastr(seed): 0.753 Number of pairs reference - predicted secondary structure: 40 Wilcoxon single-rank test P-value: 3.56938820447e-08	91 Murlet(seed) vs Mastr(seed) Matthews Correlation Coefficient Murlet(seed): 0.468 Mastr(seed): 0.467 Sensitivity Murlet(seed): 0.266 Mastr(seed): 0.278 Positive Predictive Value Murlet(seed): 0.828 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 91 Wilcoxon single-rank test P-value: 0.0563054219211	157 Alterna vs Mastr(seed) Matthews Correlation Coefficient Alterna: 0.560 Mastr(seed): 0.309 Sensitivity Alterna: 0.552 Mastr(seed): 0.118 Positive Predictive Value Alterna: 0.575 Mastr(seed): 0.815 Number of pairs reference - predicted secondary structure: 157 Wilcoxon single-rank test P-value: 3.56938820447e-08	123 Carnac(seed) vs Mastr(seed) Matthews Correlation Coefficient Carnac(seed): 0.415 Mastr(seed): 0.385 Sensitivity Carnac(seed): 0.196 Mastr(seed): 0.190 Positive Predictive Value Carnac(seed): 0.884 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 123 Wilcoxon single-rank test P-value: 3.56938820447e-08	234 Vsfold4 vs Mastr(seed) Matthews Correlation Coefficient Vsfold4: 0.368 Mastr(seed): 0.263 Sensitivity Vsfold4: 0.337 Mastr(seed): 0.089 Positive Predictive Value Vsfold4: 0.410 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08	216 RSpredict(seed) vs Mastr(seed) Matthews Correlation Coefficient RSpredict(seed): 0.373 Mastr(seed): 0.276 Sensitivity RSpredict(seed): 0.251 Mastr(seed): 0.097 Positive Predictive Value RSpredict(seed): 0.562 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 216 Wilcoxon single-rank test P-value: 3.56938820447e-08	234 Vsfold5 vs Mastr(seed) Matthews Correlation Coefficient Vsfold5: 0.328 Mastr(seed): 0.263 Sensitivity Vsfold5: 0.310 Mastr(seed): 0.089 Positive Predictive Value Vsfold5: 0.356 Mastr(seed): 0.788 Number of pairs reference - predicted secondary structure: 234 Wilcoxon single-rank test P-value: 3.56938820447e-08	157 RDfolder vs Mastr(seed) Matthews Correlation Coefficient RDfolder: 0.485 Mastr(seed): 0.309 Sensitivity RDfolder: 0.420 Mastr(seed): 0.118 Positive Predictive Value RDfolder: 0.569 Mastr(seed): 0.815 Number of pairs reference - predicted secondary structure: 157 Wilcoxon single-rank test P-value: 3.56938820447e-08	199 MCFold vs Mastr(seed) Matthews Correlation Coefficient MCFold: 0.473 Mastr(seed): 0.261 Sensitivity MCFold: 0.525 Mastr(seed): 0.084 Positive Predictive Value MCFold: 0.433 Mastr(seed): 0.822 Number of pairs reference - predicted secondary structure: 199 Wilcoxon single-rank test P-value: 3.56938820447e-08	49 NanoFolder vs Mastr(seed) Matthews Correlation Coefficient NanoFolder: 0.369 Mastr(seed): 0.191 Sensitivity NanoFolder: 0.424 Mastr(seed): 0.055 Positive Predictive Value NanoFolder: 0.330 Mastr(seed): 0.673 Number of pairs reference - predicted secondary structure: 49 Wilcoxon single-rank test P-value: 3.56938820447e-08

Matthews Correlation Coefficients (MCC) plotted for all methods in a ranking. MCCs were calculated by taking into account all reference and predicted RNA structures by a given method in the entire ranking. The plot includes only methods for which at least 40% of comparisons with other methods is valid (i.e. at least 40% of the comparisons were based on more than 10 predictions for common targets).